Matt:LabNotes/2013-7-19: Difference between revisions
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# Counts for each probe: CountsofAgi26k_0gap50bp.txt, CountsofAgi26k_0gapFull.txt, CountsofAgi26k_20gap50bp.txt, CountsofAgi26k_20gapFull.txt | # Counts for each probe: CountsofAgi26k_0gap50bp.txt, CountsofAgi26k_0gapFull.txt, CountsofAgi26k_20gap50bp.txt, CountsofAgi26k_20gapFull.txt | ||
## Many 0 gap reads aligned to 20 gap probes and vice versa suggests this method isn't specific enough | ## Many 0 gap reads aligned to 20 gap probes and vice versa suggests this method isn't specific enough | ||
Below is number of probes binned into number of reads for 50bp reference probes | |||
{| {{table}} | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''0 gap reads aligned to 0 gap probe''' | | align="center" style="background:#f0f0f0;"|'''0 gap reads aligned to 0 gap probe''' | ||
Line 259: | Line 259: | ||
|- | |- | ||
| 808.8421053||0||More||1||444.0701754||0||More||1 | | 808.8421053||0||More||1||444.0701754||0||More||1 | ||
|- | |||
| More||1||||||More||1|||| | |||
|} | |||
Below is number of probes binned into number of reads for full reference probes | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''0 gap reads aligned to 0 gap probe''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''0 gap reads aligned to 20 gap probes''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''20 gap reads aligned to 0 gap probes''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''20 gap reads aligned to 20 gap probes''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
|- | |||
| Bin||Frequency||Bin||Frequency||Bin||Frequency||Bin||Frequency | |||
|- | |||
| 1||1||0||26||0||98||20||1 | |||
|- | |||
| 14.92982456||80||10.94690265||3858||15.01754386||7662||38.48672566||1 | |||
|- | |||
| 28.85964912||42||21.89380531||3605||30.03508772||2922||56.97345133||5 | |||
|- | |||
| 42.78947368||31||32.84070796||1623||45.05263158||1150||75.46017699||9 | |||
|- | |||
| 56.71929825||26||43.78761062||999||60.07017544||484||93.94690265||16 | |||
|- | |||
| 70.64912281||18||54.73451327||761||75.0877193||231||112.4336283||13 | |||
|- | |||
| 84.57894737||12||65.68141593||496||90.10526316||135||130.920354||15 | |||
|- | |||
| 98.50877193||7||76.62831858||354||105.122807||82||149.4070796||19 | |||
|- | |||
| 112.4385965||11||87.57522124||270||120.1403509||39||167.8938053||15 | |||
|- | |||
| 126.3684211||7||98.52212389||204||135.1578947||24||186.380531||20 | |||
|- | |||
| 140.2982456||6||109.4690265||141||150.1754386||20||204.8672566||34 | |||
|- | |||
| 154.2280702||9||120.4159292||106||165.1929825||13||223.3539823||57 | |||
|- | |||
| 168.1578947||3||131.3628319||78||180.2105263||7||241.840708||62 | |||
|- | |||
| 182.0877193||8||142.3097345||74||195.2280702||4||260.3274336||135 | |||
|- | |||
| 196.0175439||9||153.2566372||54||210.245614||9||278.8141593||195 | |||
|- | |||
| 209.9473684||12||164.2035398||39||225.2631579||11||297.300885||328 | |||
|- | |||
| 223.877193||14||175.1504425||33||240.2807018||9||315.7876106||458 | |||
|- | |||
| 237.8070175||16||186.0973451||31||255.2982456||3||334.2743363||664 | |||
|- | |||
| 251.7368421||14||197.0442478||10||270.3157895||11||352.7610619||731 | |||
|- | |||
| 265.6666667||21||207.9911504||13||285.3333333||2||371.2477876||991 | |||
|- | |||
| 279.5964912||34||218.9380531||14||300.3508772||11||389.7345133||1022 | |||
|- | |||
| 293.5263158||37||229.8849558||11||315.3684211||12||408.2212389||1133 | |||
|- | |||
| 307.4561404||44||240.8318584||16||330.3859649||16||426.7079646||1077 | |||
|- | |||
| 321.3859649||73||251.7787611||8||345.4035088||22||445.1946903||1074 | |||
|- | |||
| 335.3157895||83||262.7256637||9||360.4210526||14||463.6814159||993 | |||
|- | |||
| 349.245614||122||273.6725664||11||375.4385965||34||482.1681416||887 | |||
|- | |||
| 363.1754386||145||284.619469||9||390.4561404||23||500.6548673||682 | |||
|- | |||
| 377.1052632||199||295.5663717||6||405.4736842||19||519.1415929||601 | |||
|- | |||
| 391.0350877||220||306.5132743||7||420.4912281||23||537.6283186||433 | |||
|- | |||
| 404.9649123||276||317.460177||5||435.5087719||25||556.1150442||342 | |||
|- | |||
| 418.8947368||343||328.4070796||5||450.5263158||11||574.6017699||249 | |||
|- | |||
| 432.8245614||438||339.3539823||3||465.5438596||6||593.0884956||182 | |||
|- | |||
| 446.754386||460||350.300885||1||480.5614035||4||611.5752212||145 | |||
|- | |||
| 460.6842105||562||361.2477876||0||495.5789474||9||630.0619469||95 | |||
|- | |||
| 474.6140351||580||372.1946903||5||510.5964912||12||648.5486726||70 | |||
|- | |||
| 488.5438596||612||383.1415929||4||525.6140351||3||667.0353982||43 | |||
|- | |||
| 502.4736842||678||394.0884956||3||540.6315789||6||685.5221239||47 | |||
|- | |||
| 516.4035088||608||405.0353982||2||555.6491228||2||704.0088496||32 | |||
|- | |||
| 530.3333333||715||415.9823009||0||570.6666667||2||722.4955752||22 | |||
|- | |||
| 544.2631579||626||426.9292035||1||585.6842105||0||740.9823009||19 | |||
|- | |||
| 558.1929825||702||437.8761062||2||600.7017544||4||759.4690265||13 | |||
|- | |||
| 572.122807||664||448.8230088||2||615.7192982||1||777.9557522||6 | |||
|- | |||
| 586.0526316||628||459.7699115||1||630.7368421||0||796.4424779||6 | |||
|- | |||
| 599.9824561||502||470.7168142||7||645.754386||1||814.9292035||4 | |||
|- | |||
| 613.9122807||456||481.6637168||6||660.7719298||1||833.4159292||2 | |||
|- | |||
| 627.8421053||480||492.6106195||1||675.7894737||0||851.9026549||1 | |||
|- | |||
| 641.7719298||363||503.5575221||2||690.8070175||0||870.3893805||4 | |||
|- | |||
| 655.7017544||319||514.5044248||1||705.8245614||0||888.8761062||1 | |||
|- | |||
| 669.6315789||258||525.4513274||0||720.8421053||0||907.3628319||1 | |||
|- | |||
| 683.5614035||276||536.3982301||0||735.8596491||0||925.8495575||1 | |||
|- | |||
| 697.4912281||215||547.3451327||3||750.877193||0||944.3362832||1 | |||
|- | |||
| 711.4210526||199||558.2920354||4||765.8947368||0||962.8230088||1 | |||
|- | |||
| 725.3508772||159||569.2389381||2||780.9122807||0||981.3097345||1 | |||
|- | |||
| 739.2807018||119||580.1858407||2||795.9298246||0||999.7964602||0 | |||
|- | |||
| 753.2105263||126||591.1327434||2||810.9473684||0||1018.283186||1 | |||
|- | |||
| 767.1403509||71||602.079646||4||825.9649123||1||1036.769912||0 | |||
|- | |||
| 781.0701754||83||613.0265487||0||840.9824561||0||1055.256637||0 | |||
|- | |||
| 795||48||623.9734513||3||856||0||1073.743363||0 | |||
|- | |||
| 808.9298246||28||634.920354||1||871.0175439||0||1092.230088||0 | |||
|- | |||
| 822.8596491||32||645.8672566||2||886.0350877||0||1110.716814||0 | |||
|- | |||
| 836.7894737||30||656.8141593||2||901.0526316||0||1129.20354||0 | |||
|- | |||
| 850.7192982||29||667.7610619||3||916.0701754||0||1147.690265||0 | |||
|- | |||
| 864.6491228||22||678.7079646||3||931.0877193||0||1166.176991||0 | |||
|- | |||
| 878.5789474||23||689.6548673||0||946.1052632||0||1184.663717||0 | |||
|- | |||
| 892.5087719||15||700.6017699||1||961.122807||0||1203.150442||1 | |||
|- | |||
| 906.4385965||11||711.5486726||3||976.1403509||0||1221.637168||0 | |||
|- | |||
| 920.3684211||9||722.4955752||2||991.1578947||0||1240.123894||0 | |||
|- | |||
| 934.2982456||8||733.4424779||3||1006.175439||0||1258.610619||0 | |||
|- | |||
| 948.2280702||8||744.3893805||0||1021.192982||0||1277.097345||0 | |||
|- | |||
| 962.1578947||9||755.3362832||1||1036.210526||0||1295.584071||0 | |||
|- | |||
| 976.0877193||5||766.2831858||1||1051.22807||0||1314.070796||0 | |||
|- | |||
| 990.0175439||7||777.2300885||0||1066.245614||0||1332.557522||1 | |||
|- | |||
| 1003.947368||5||788.1769912||2||1081.263158||0||1351.044248||0 | |||
|- | |||
| 1017.877193||2||799.1238938||1||1096.280702||0||1369.530973||0 | |||
|- | |||
| 1031.807018||0||810.0707965||0||1111.298246||0||1388.017699||0 | |||
|- | |||
| 1045.736842||5||821.0176991||0||1126.315789||0||1406.504425||0 | |||
|- | |||
| 1059.666667||2||831.9646018||0||1141.333333||0||1424.99115||0 | |||
|- | |||
| 1073.596491||2||842.9115044||0||1156.350877||0||1443.477876||0 | |||
|- | |||
| 1087.526316||2||853.8584071||0||1171.368421||0||1461.964602||0 | |||
|- | |||
| 1101.45614||3||864.8053097||0||1186.385965||0||1480.451327||0 | |||
|- | |||
| 1115.385965||3||875.7522124||0||1201.403509||0||1498.938053||0 | |||
|- | |||
| 1129.315789||3||886.699115||0||1216.421053||0||1517.424779||0 | |||
|- | |||
| 1143.245614||0||897.6460177||0||1231.438596||0||1535.911504||0 | |||
|- | |||
| 1157.175439||3||908.5929204||0||1246.45614||0||1554.39823||0 | |||
|- | |||
| 1171.105263||3||919.539823||0||1261.473684||0||1572.884956||0 | |||
|- | |||
| 1185.035088||2||930.4867257||0||1276.491228||0||1591.371681||0 | |||
|- | |||
| 1198.964912||2||941.4336283||0||1291.508772||0||1609.858407||0 | |||
|- | |||
| 1212.894737||2||952.380531||0||1306.526316||0||1628.345133||0 | |||
|- | |||
| 1226.824561||4||963.3274336||0||1321.54386||0||1646.831858||0 | |||
|- | |||
| 1240.754386||7||974.2743363||0||1336.561404||0||1665.318584||0 | |||
|- | |||
| 1254.684211||2||985.2212389||0||1351.578947||0||1683.80531||0 | |||
|- | |||
| 1268.614035||2||996.1681416||0||1366.596491||0||1702.292035||0 | |||
|- | |||
| 1282.54386||4||1007.115044||0||1381.614035||0||1720.778761||0 | |||
|- | |||
| 1296.473684||2||1018.061947||0||1396.631579||0||1739.265487||0 | |||
|- | |||
| 1310.403509||0||1029.00885||0||1411.649123||0||1757.752212||0 | |||
|- | |||
| 1324.333333||1||1039.955752||0||1426.666667||0||1776.238938||0 | |||
|- | |||
| 1338.263158||1||1050.902655||0||1441.684211||0||1794.725664||0 | |||
|- | |||
| 1352.192982||0||1061.849558||0||1456.701754||0||1813.212389||0 | |||
|- | |||
| 1366.122807||1||1072.79646||0||1471.719298||0||1831.699115||0 | |||
|- | |||
| 1380.052632||1||1083.743363||0||1486.736842||0||1850.185841||0 | |||
|- | |||
| 1393.982456||2||1094.690265||0||1501.754386||0||1868.672566||0 | |||
|- | |||
| 1407.912281||0||1105.637168||0||1516.77193||0||1887.159292||0 | |||
|- | |||
| 1421.842105||2||1116.584071||0||1531.789474||0||1905.646018||0 | |||
|- | |||
| 1435.77193||1||1127.530973||0||1546.807018||0||1924.132743||0 | |||
|- | |||
| 1449.701754||0||1138.477876||0||1561.824561||0||1942.619469||0 | |||
|- | |||
| 1463.631579||1||1149.424779||0||1576.842105||0||1961.106195||0 | |||
|- | |||
| 1477.561404||1||1160.371681||0||1591.859649||0||1979.59292||0 | |||
|- | |||
| 1491.491228||0||1171.318584||0||1606.877193||0||1998.079646||0 | |||
|- | |||
| 1505.421053||0||1182.265487||0||1621.894737||0||2016.566372||0 | |||
|- | |||
| 1519.350877||0||1193.212389||0||1636.912281||0||2035.053097||0 | |||
|- | |||
| 1533.280702||0||1204.159292||0||1651.929825||0||2053.539823||0 | |||
|- | |||
| 1547.210526||0||1215.106195||0||1666.947368||0||2072.026549||0 | |||
|- | |||
| 1561.140351||1||1226.053097||0||1681.964912||0||2090.513274||0 | |||
|- | |||
| 1575.070175||0||More||1||1696.982456||0||More||1 | |||
|- | |- | ||
| More||1||||||More||1|||| | | More||1||||||More||1|||| | ||
|} | |} |
Latest revision as of 21:59, 22 July 2013
Analysis of HL155: Representation Bias of Agi26k Oligos[edit]
- Previously amplified Agi26k oligos with sequence adapters to sequence
- By counting the number of reads for each probe, can determine uniformity of oligos in probe set
- Turn FISSEQ_Probes_Dec2012.txt into fasta file (Full: Agi26kprobes_to_order.fa 50bp: Agi26kprobes_to_order_50bp.fa)
- First Primer for V6: "GTCATATCGGTCACTGTT"
- First Primer for V4: "TAGACTGGAAGAGCACTGTT"
- Build index for probes
- /home/kunzhang/softwares/bowtie2-latest/bowtie2-build ~/InSitu_HL155_130628_Analysis/Agi26kprobes_to_order.fa Agi26kprobes
- /home/kunzhang/softwares/bowtie2-latest/bowtie2-build ~/InSitu_HL155_130628_Analysis/Agi26kprobes_to_order_50bp.fa Agi26kprobes_50bp
- Align to index
- Indx10 -> 0 gap -> V6:
- /home/kunzhang/softwares/bowtie2-latest/bowtie2 -k 1 --phred64 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26kprobes -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx10.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2probes_0gapFull.txt &
16368416 reads; of these:
16368416 (100.00%) were unpaired; of these:
8915822 (54.47%) aligned 0 times
7452594 (45.53%) aligned exactly 1 time
0 (0.00%) aligned >1 times
45.53% overall alignment rate - /home/kunzhang/softwares/bowtie2-latest/bowtie2 -k 1 --phred64 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26kprobes_50bp -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx10.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2probes_0gap50bp.txt &
mzcai@genome-miner:~/InSitu_HL155_130628_Analysis$ 16368416 reads; of these:
16368416 (100.00%) were unpaired; of these:
15978678 (97.62%) aligned 0 times
389738 (2.38%) aligned exactly 1 time
0 (0.00%) aligned >1 times
2.38% overall alignment rate
- /home/kunzhang/softwares/bowtie2-latest/bowtie2 -k 1 --phred64 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26kprobes -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx10.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2probes_0gapFull.txt &
- Indx12 -> 20 gap -> V4:
- /home/kunzhang/softwares/bowtie2-latest/bowtie2 -k 1 --phred64 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26kprobes -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx12.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2probes_20gapFull.txt &
mzcai@genome-miner:~/InSitu_HL155_130628_Analysis$ 17308686 reads; of these:
17308686 (100.00%) were unpaired; of these:
11482192 (66.34%) aligned 0 times
5826494 (33.66%) aligned exactly 1 time
0 (0.00%) aligned >1 times
33.66% overall alignment rate - /home/kunzhang/softwares/bowtie2-latest/bowtie2 -k 1 --phred64 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26kprobes_50bp -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx12.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2probes_20gap50bp.txt &
mzcai@genome-miner:~/InSitu_HL155_130628_Analysis$ 17308686 reads; of these:
17308686 (100.00%) were unpaired; of these:
17112441 (98.87%) aligned 0 times
196245 (1.13%) aligned exactly 1 time
0 (0.00%) aligned >1 times
1.13% overall alignment rate
- /home/kunzhang/softwares/bowtie2-latest/bowtie2 -k 1 --phred64 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26kprobes -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx12.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2probes_20gapFull.txt &
- Indx10 -> 0 gap -> V6:
- Counts for each probe: CountsofAgi26k_0gap50bp.txt, CountsofAgi26k_0gapFull.txt, CountsofAgi26k_20gap50bp.txt, CountsofAgi26k_20gapFull.txt
- Many 0 gap reads aligned to 20 gap probes and vice versa suggests this method isn't specific enough
Below is number of probes binned into number of reads for 50bp reference probes
0 gap reads aligned to 0 gap probe | ' | 0 gap reads aligned to 20 gap probes | ' | 20 gap reads aligned to 0 gap probes | ' | 20 gap reads aligned to 20 gap probes | ' |
Bin | Frequency | Bin | Frequency | Bin | Frequency | Bin | Frequency |
0 | 19 | 0 | 1317 | 0 | 4034 | 0 | 5 |
7.157894737 | 293 | 19.10619469 | 11167 | 3.929824561 | 7384 | 9.902654867 | 4268 |
14.31578947 | 1427 | 38.21238938 | 310 | 7.859649123 | 1185 | 19.80530973 | 7286 |
21.47368421 | 3791 | 57.31858407 | 73 | 11.78947368 | 289 | 29.7079646 | 1191 |
28.63157895 | 4282 | 76.42477876 | 31 | 15.71929825 | 135 | 39.61061947 | 111 |
35.78947368 | 2293 | 95.53097345 | 20 | 19.64912281 | 57 | 49.51327434 | 37 |
42.94736842 | 783 | 114.6371681 | 12 | 23.57894737 | 30 | 59.4159292 | 19 |
50.10526316 | 186 | 133.7433628 | 8 | 27.50877193 | 20 | 69.31858407 | 13 |
57.26315789 | 37 | 152.8495575 | 2 | 31.43859649 | 8 | 79.22123894 | 8 |
64.42105263 | 12 | 171.9557522 | 3 | 35.36842105 | 4 | 89.12389381 | 4 |
71.57894737 | 19 | 191.0619469 | 1 | 39.29824561 | 4 | 99.02654867 | 3 |
78.73684211 | 8 | 210.1681416 | 3 | 43.22807018 | 6 | 108.9292035 | 0 |
85.89473684 | 10 | 229.2743363 | 2 | 47.15789474 | 3 | 118.8318584 | 1 |
93.05263158 | 6 | 248.380531 | 3 | 51.0877193 | 0 | 128.7345133 | 2 |
100.2105263 | 4 | 267.4867257 | 1 | 55.01754386 | 0 | 138.6371681 | 2 |
107.3684211 | 1 | 286.5929204 | 1 | 58.94736842 | 3 | 148.539823 | 0 |
114.5263158 | 1 | 305.699115 | 0 | 62.87719298 | 1 | 158.4424779 | 5 |
121.6842105 | 1 | 324.8053097 | 1 | 66.80701754 | 0 | 168.3451327 | 1 |
128.8421053 | 0 | 343.9115044 | 1 | 70.73684211 | 3 | 178.2477876 | 0 |
136 | 0 | 363.0176991 | 0 | 74.66666667 | 0 | 188.1504425 | 0 |
143.1578947 | 0 | 382.1238938 | 1 | 78.59649123 | 0 | 198.0530973 | 0 |
150.3157895 | 0 | 401.2300885 | 0 | 82.52631579 | 0 | 207.9557522 | 0 |
157.4736842 | 0 | 420.3362832 | 0 | 86.45614035 | 0 | 217.8584071 | 1 |
164.6315789 | 0 | 439.4424779 | 1 | 90.38596491 | 1 | 227.7610619 | 0 |
171.7894737 | 1 | 458.5486726 | 0 | 94.31578947 | 0 | 237.6637168 | 0 |
178.9473684 | 0 | 477.6548673 | 0 | 98.24561404 | 0 | 247.5663717 | 0 |
186.1052632 | 1 | 496.7610619 | 0 | 102.1754386 | 0 | 257.4690265 | 1 |
193.2631579 | 0 | 515.8672566 | 0 | 106.1052632 | 1 | 267.3716814 | 1 |
200.4210526 | 0 | 534.9734513 | 0 | 110.0350877 | 1 | 277.2743363 | 0 |
207.5789474 | 0 | 554.079646 | 0 | 113.9649123 | 0 | 287.1769912 | 0 |
214.7368421 | 0 | 573.1858407 | 1 | 117.8947368 | 1 | 297.079646 | 0 |
221.8947368 | 0 | 592.2920354 | 0 | 121.8245614 | 2 | 306.9823009 | 0 |
229.0526316 | 0 | 611.3982301 | 0 | 125.754386 | 1 | 316.8849558 | 0 |
236.2105263 | 0 | 630.5044248 | 0 | 129.6842105 | 0 | 326.7876106 | 0 |
243.3684211 | 0 | 649.6106195 | 1 | 133.6140351 | 0 | 336.6902655 | 1 |
250.5263158 | 0 | 668.7168142 | 0 | 137.5438596 | 0 | 346.5929204 | 0 |
257.6842105 | 0 | 687.8230088 | 0 | 141.4736842 | 1 | 356.4955752 | 0 |
264.8421053 | 1 | 706.9292035 | 0 | 145.4035088 | 0 | 366.3982301 | 0 |
272 | 0 | 726.0353982 | 0 | 149.3333333 | 0 | 376.300885 | 0 |
279.1578947 | 0 | 745.1415929 | 0 | 153.2631579 | 1 | 386.2035398 | 0 |
286.3157895 | 0 | 764.2477876 | 0 | 157.1929825 | 2 | 396.1061947 | 0 |
293.4736842 | 0 | 783.3539823 | 0 | 161.122807 | 0 | 406.0088496 | 0 |
300.6315789 | 0 | 802.460177 | 0 | 165.0526316 | 0 | 415.9115044 | 0 |
307.7894737 | 0 | 821.5663717 | 0 | 168.9824561 | 0 | 425.8141593 | 0 |
314.9473684 | 0 | 840.6725664 | 0 | 172.9122807 | 0 | 435.7168142 | 0 |
322.1052632 | 0 | 859.7787611 | 0 | 176.8421053 | 0 | 445.619469 | 0 |
329.2631579 | 0 | 878.8849558 | 0 | 180.7719298 | 0 | 455.5221239 | 0 |
336.4210526 | 0 | 897.9911504 | 0 | 184.7017544 | 1 | 465.4247788 | 0 |
343.5789474 | 1 | 917.0973451 | 0 | 188.6315789 | 0 | 475.3274336 | 0 |
350.7368421 | 0 | 936.2035398 | 0 | 192.5614035 | 0 | 485.2300885 | 0 |
357.8947368 | 0 | 955.3097345 | 0 | 196.4912281 | 0 | 495.1327434 | 0 |
365.0526316 | 0 | 974.4159292 | 0 | 200.4210526 | 0 | 505.0353982 | 0 |
372.2105263 | 0 | 993.5221239 | 0 | 204.3508772 | 0 | 514.9380531 | 0 |
379.3684211 | 0 | 1012.628319 | 0 | 208.2807018 | 0 | 524.840708 | 0 |
386.5263158 | 0 | 1031.734513 | 0 | 212.2105263 | 0 | 534.7433628 | 0 |
393.6842105 | 1 | 1050.840708 | 0 | 216.1403509 | 0 | 544.6460177 | 0 |
400.8421053 | 0 | 1069.946903 | 0 | 220.0701754 | 0 | 554.5486726 | 0 |
408 | 0 | 1089.053097 | 0 | 224 | 0 | 564.4513274 | 1 |
415.1578947 | 0 | 1108.159292 | 0 | 227.9298246 | 0 | 574.3539823 | 0 |
422.3157895 | 0 | 1127.265487 | 0 | 231.8596491 | 0 | 584.2566372 | 0 |
429.4736842 | 0 | 1146.371681 | 1 | 235.7894737 | 0 | 594.159292 | 0 |
436.6315789 | 0 | 1165.477876 | 0 | 239.7192982 | 0 | 604.0619469 | 0 |
443.7894737 | 0 | 1184.584071 | 0 | 243.6491228 | 0 | 613.9646018 | 0 |
450.9473684 | 0 | 1203.690265 | 0 | 247.5789474 | 0 | 623.8672566 | 0 |
458.1052632 | 0 | 1222.79646 | 0 | 251.5087719 | 0 | 633.7699115 | 0 |
465.2631579 | 0 | 1241.902655 | 0 | 255.4385965 | 0 | 643.6725664 | 0 |
472.4210526 | 0 | 1261.00885 | 0 | 259.3684211 | 0 | 653.5752212 | 0 |
479.5789474 | 0 | 1280.115044 | 0 | 263.2982456 | 0 | 663.4778761 | 0 |
486.7368421 | 0 | 1299.221239 | 0 | 267.2280702 | 0 | 673.380531 | 0 |
493.8947368 | 0 | 1318.327434 | 0 | 271.1578947 | 0 | 683.2831858 | 0 |
501.0526316 | 0 | 1337.433628 | 0 | 275.0877193 | 0 | 693.1858407 | 0 |
508.2105263 | 0 | 1356.539823 | 0 | 279.0175439 | 0 | 703.0884956 | 0 |
515.3684211 | 0 | 1375.646018 | 0 | 282.9473684 | 0 | 712.9911504 | 0 |
522.5263158 | 0 | 1394.752212 | 0 | 286.877193 | 0 | 722.8938053 | 0 |
529.6842105 | 0 | 1413.858407 | 0 | 290.8070175 | 0 | 732.7964602 | 0 |
536.8421053 | 0 | 1432.964602 | 0 | 294.7368421 | 0 | 742.699115 | 0 |
544 | 0 | 1452.070796 | 0 | 298.6666667 | 0 | 752.6017699 | 0 |
551.1578947 | 0 | 1471.176991 | 0 | 302.5964912 | 0 | 762.5044248 | 0 |
558.3157895 | 0 | 1490.283186 | 0 | 306.5263158 | 0 | 772.4070796 | 0 |
565.4736842 | 0 | 1509.389381 | 0 | 310.4561404 | 0 | 782.3097345 | 1 |
572.6315789 | 0 | 1528.495575 | 0 | 314.3859649 | 0 | 792.2123894 | 0 |
579.7894737 | 0 | 1547.60177 | 0 | 318.3157895 | 0 | 802.1150442 | 0 |
586.9473684 | 0 | 1566.707965 | 0 | 322.245614 | 0 | 812.0176991 | 0 |
594.1052632 | 0 | 1585.814159 | 0 | 326.1754386 | 0 | 821.920354 | 0 |
601.2631579 | 0 | 1604.920354 | 0 | 330.1052632 | 0 | 831.8230088 | 0 |
608.4210526 | 0 | 1624.026549 | 0 | 334.0350877 | 0 | 841.7256637 | 0 |
615.5789474 | 0 | 1643.132743 | 0 | 337.9649123 | 0 | 851.6283186 | 0 |
622.7368421 | 0 | 1662.238938 | 0 | 341.8947368 | 0 | 861.5309735 | 0 |
629.8947368 | 0 | 1681.345133 | 0 | 345.8245614 | 0 | 871.4336283 | 0 |
637.0526316 | 0 | 1700.451327 | 0 | 349.754386 | 0 | 881.3362832 | 0 |
644.2105263 | 0 | 1719.557522 | 0 | 353.6842105 | 0 | 891.2389381 | 0 |
651.3684211 | 0 | 1738.663717 | 0 | 357.6140351 | 0 | 901.1415929 | 0 |
658.5263158 | 0 | 1757.769912 | 0 | 361.5438596 | 0 | 911.0442478 | 0 |
665.6842105 | 0 | 1776.876106 | 0 | 365.4736842 | 0 | 920.9469027 | 0 |
672.8421053 | 0 | 1795.982301 | 0 | 369.4035088 | 0 | 930.8495575 | 0 |
680 | 0 | 1815.088496 | 0 | 373.3333333 | 0 | 940.7522124 | 0 |
687.1578947 | 0 | 1834.19469 | 0 | 377.2631579 | 0 | 950.6548673 | 0 |
694.3157895 | 0 | 1853.300885 | 1 | 381.1929825 | 0 | 960.5575221 | 0 |
701.4736842 | 0 | 1872.40708 | 0 | 385.122807 | 0 | 970.460177 | 0 |
708.6315789 | 0 | 1891.513274 | 0 | 389.0526316 | 0 | 980.3628319 | 0 |
715.7894737 | 0 | 1910.619469 | 0 | 392.9824561 | 0 | 990.2654867 | 0 |
722.9473684 | 0 | 1929.725664 | 0 | 396.9122807 | 0 | 1000.168142 | 0 |
730.1052632 | 0 | 1948.831858 | 0 | 400.8421053 | 0 | 1010.070796 | 0 |
737.2631579 | 0 | 1967.938053 | 0 | 404.7719298 | 0 | 1019.973451 | 0 |
744.4210526 | 0 | 1987.044248 | 0 | 408.7017544 | 0 | 1029.876106 | 0 |
751.5789474 | 0 | 2006.150442 | 0 | 412.6315789 | 0 | 1039.778761 | 0 |
758.7368421 | 0 | 2025.256637 | 0 | 416.5614035 | 0 | 1049.681416 | 0 |
765.8947368 | 0 | 2044.362832 | 0 | 420.4912281 | 0 | 1059.584071 | 0 |
773.0526316 | 0 | 2063.469027 | 0 | 424.4210526 | 0 | 1069.486726 | 0 |
780.2105263 | 0 | 2082.575221 | 0 | 428.3508772 | 0 | 1079.389381 | 0 |
787.3684211 | 0 | 2101.681416 | 0 | 432.2807018 | 0 | 1089.292035 | 0 |
794.5263158 | 0 | 2120.787611 | 0 | 436.2105263 | 0 | 1099.19469 | 0 |
801.6842105 | 0 | 2139.893805 | 0 | 440.1403509 | 0 | 1109.097345 | 0 |
808.8421053 | 0 | More | 1 | 444.0701754 | 0 | More | 1 |
More | 1 | More | 1 |
Below is number of probes binned into number of reads for full reference probes
0 gap reads aligned to 0 gap probe | ' | 0 gap reads aligned to 20 gap probes | ' | 20 gap reads aligned to 0 gap probes | ' | 20 gap reads aligned to 20 gap probes | ' |
Bin | Frequency | Bin | Frequency | Bin | Frequency | Bin | Frequency |
1 | 1 | 0 | 26 | 0 | 98 | 20 | 1 |
14.92982456 | 80 | 10.94690265 | 3858 | 15.01754386 | 7662 | 38.48672566 | 1 |
28.85964912 | 42 | 21.89380531 | 3605 | 30.03508772 | 2922 | 56.97345133 | 5 |
42.78947368 | 31 | 32.84070796 | 1623 | 45.05263158 | 1150 | 75.46017699 | 9 |
56.71929825 | 26 | 43.78761062 | 999 | 60.07017544 | 484 | 93.94690265 | 16 |
70.64912281 | 18 | 54.73451327 | 761 | 75.0877193 | 231 | 112.4336283 | 13 |
84.57894737 | 12 | 65.68141593 | 496 | 90.10526316 | 135 | 130.920354 | 15 |
98.50877193 | 7 | 76.62831858 | 354 | 105.122807 | 82 | 149.4070796 | 19 |
112.4385965 | 11 | 87.57522124 | 270 | 120.1403509 | 39 | 167.8938053 | 15 |
126.3684211 | 7 | 98.52212389 | 204 | 135.1578947 | 24 | 186.380531 | 20 |
140.2982456 | 6 | 109.4690265 | 141 | 150.1754386 | 20 | 204.8672566 | 34 |
154.2280702 | 9 | 120.4159292 | 106 | 165.1929825 | 13 | 223.3539823 | 57 |
168.1578947 | 3 | 131.3628319 | 78 | 180.2105263 | 7 | 241.840708 | 62 |
182.0877193 | 8 | 142.3097345 | 74 | 195.2280702 | 4 | 260.3274336 | 135 |
196.0175439 | 9 | 153.2566372 | 54 | 210.245614 | 9 | 278.8141593 | 195 |
209.9473684 | 12 | 164.2035398 | 39 | 225.2631579 | 11 | 297.300885 | 328 |
223.877193 | 14 | 175.1504425 | 33 | 240.2807018 | 9 | 315.7876106 | 458 |
237.8070175 | 16 | 186.0973451 | 31 | 255.2982456 | 3 | 334.2743363 | 664 |
251.7368421 | 14 | 197.0442478 | 10 | 270.3157895 | 11 | 352.7610619 | 731 |
265.6666667 | 21 | 207.9911504 | 13 | 285.3333333 | 2 | 371.2477876 | 991 |
279.5964912 | 34 | 218.9380531 | 14 | 300.3508772 | 11 | 389.7345133 | 1022 |
293.5263158 | 37 | 229.8849558 | 11 | 315.3684211 | 12 | 408.2212389 | 1133 |
307.4561404 | 44 | 240.8318584 | 16 | 330.3859649 | 16 | 426.7079646 | 1077 |
321.3859649 | 73 | 251.7787611 | 8 | 345.4035088 | 22 | 445.1946903 | 1074 |
335.3157895 | 83 | 262.7256637 | 9 | 360.4210526 | 14 | 463.6814159 | 993 |
349.245614 | 122 | 273.6725664 | 11 | 375.4385965 | 34 | 482.1681416 | 887 |
363.1754386 | 145 | 284.619469 | 9 | 390.4561404 | 23 | 500.6548673 | 682 |
377.1052632 | 199 | 295.5663717 | 6 | 405.4736842 | 19 | 519.1415929 | 601 |
391.0350877 | 220 | 306.5132743 | 7 | 420.4912281 | 23 | 537.6283186 | 433 |
404.9649123 | 276 | 317.460177 | 5 | 435.5087719 | 25 | 556.1150442 | 342 |
418.8947368 | 343 | 328.4070796 | 5 | 450.5263158 | 11 | 574.6017699 | 249 |
432.8245614 | 438 | 339.3539823 | 3 | 465.5438596 | 6 | 593.0884956 | 182 |
446.754386 | 460 | 350.300885 | 1 | 480.5614035 | 4 | 611.5752212 | 145 |
460.6842105 | 562 | 361.2477876 | 0 | 495.5789474 | 9 | 630.0619469 | 95 |
474.6140351 | 580 | 372.1946903 | 5 | 510.5964912 | 12 | 648.5486726 | 70 |
488.5438596 | 612 | 383.1415929 | 4 | 525.6140351 | 3 | 667.0353982 | 43 |
502.4736842 | 678 | 394.0884956 | 3 | 540.6315789 | 6 | 685.5221239 | 47 |
516.4035088 | 608 | 405.0353982 | 2 | 555.6491228 | 2 | 704.0088496 | 32 |
530.3333333 | 715 | 415.9823009 | 0 | 570.6666667 | 2 | 722.4955752 | 22 |
544.2631579 | 626 | 426.9292035 | 1 | 585.6842105 | 0 | 740.9823009 | 19 |
558.1929825 | 702 | 437.8761062 | 2 | 600.7017544 | 4 | 759.4690265 | 13 |
572.122807 | 664 | 448.8230088 | 2 | 615.7192982 | 1 | 777.9557522 | 6 |
586.0526316 | 628 | 459.7699115 | 1 | 630.7368421 | 0 | 796.4424779 | 6 |
599.9824561 | 502 | 470.7168142 | 7 | 645.754386 | 1 | 814.9292035 | 4 |
613.9122807 | 456 | 481.6637168 | 6 | 660.7719298 | 1 | 833.4159292 | 2 |
627.8421053 | 480 | 492.6106195 | 1 | 675.7894737 | 0 | 851.9026549 | 1 |
641.7719298 | 363 | 503.5575221 | 2 | 690.8070175 | 0 | 870.3893805 | 4 |
655.7017544 | 319 | 514.5044248 | 1 | 705.8245614 | 0 | 888.8761062 | 1 |
669.6315789 | 258 | 525.4513274 | 0 | 720.8421053 | 0 | 907.3628319 | 1 |
683.5614035 | 276 | 536.3982301 | 0 | 735.8596491 | 0 | 925.8495575 | 1 |
697.4912281 | 215 | 547.3451327 | 3 | 750.877193 | 0 | 944.3362832 | 1 |
711.4210526 | 199 | 558.2920354 | 4 | 765.8947368 | 0 | 962.8230088 | 1 |
725.3508772 | 159 | 569.2389381 | 2 | 780.9122807 | 0 | 981.3097345 | 1 |
739.2807018 | 119 | 580.1858407 | 2 | 795.9298246 | 0 | 999.7964602 | 0 |
753.2105263 | 126 | 591.1327434 | 2 | 810.9473684 | 0 | 1018.283186 | 1 |
767.1403509 | 71 | 602.079646 | 4 | 825.9649123 | 1 | 1036.769912 | 0 |
781.0701754 | 83 | 613.0265487 | 0 | 840.9824561 | 0 | 1055.256637 | 0 |
795 | 48 | 623.9734513 | 3 | 856 | 0 | 1073.743363 | 0 |
808.9298246 | 28 | 634.920354 | 1 | 871.0175439 | 0 | 1092.230088 | 0 |
822.8596491 | 32 | 645.8672566 | 2 | 886.0350877 | 0 | 1110.716814 | 0 |
836.7894737 | 30 | 656.8141593 | 2 | 901.0526316 | 0 | 1129.20354 | 0 |
850.7192982 | 29 | 667.7610619 | 3 | 916.0701754 | 0 | 1147.690265 | 0 |
864.6491228 | 22 | 678.7079646 | 3 | 931.0877193 | 0 | 1166.176991 | 0 |
878.5789474 | 23 | 689.6548673 | 0 | 946.1052632 | 0 | 1184.663717 | 0 |
892.5087719 | 15 | 700.6017699 | 1 | 961.122807 | 0 | 1203.150442 | 1 |
906.4385965 | 11 | 711.5486726 | 3 | 976.1403509 | 0 | 1221.637168 | 0 |
920.3684211 | 9 | 722.4955752 | 2 | 991.1578947 | 0 | 1240.123894 | 0 |
934.2982456 | 8 | 733.4424779 | 3 | 1006.175439 | 0 | 1258.610619 | 0 |
948.2280702 | 8 | 744.3893805 | 0 | 1021.192982 | 0 | 1277.097345 | 0 |
962.1578947 | 9 | 755.3362832 | 1 | 1036.210526 | 0 | 1295.584071 | 0 |
976.0877193 | 5 | 766.2831858 | 1 | 1051.22807 | 0 | 1314.070796 | 0 |
990.0175439 | 7 | 777.2300885 | 0 | 1066.245614 | 0 | 1332.557522 | 1 |
1003.947368 | 5 | 788.1769912 | 2 | 1081.263158 | 0 | 1351.044248 | 0 |
1017.877193 | 2 | 799.1238938 | 1 | 1096.280702 | 0 | 1369.530973 | 0 |
1031.807018 | 0 | 810.0707965 | 0 | 1111.298246 | 0 | 1388.017699 | 0 |
1045.736842 | 5 | 821.0176991 | 0 | 1126.315789 | 0 | 1406.504425 | 0 |
1059.666667 | 2 | 831.9646018 | 0 | 1141.333333 | 0 | 1424.99115 | 0 |
1073.596491 | 2 | 842.9115044 | 0 | 1156.350877 | 0 | 1443.477876 | 0 |
1087.526316 | 2 | 853.8584071 | 0 | 1171.368421 | 0 | 1461.964602 | 0 |
1101.45614 | 3 | 864.8053097 | 0 | 1186.385965 | 0 | 1480.451327 | 0 |
1115.385965 | 3 | 875.7522124 | 0 | 1201.403509 | 0 | 1498.938053 | 0 |
1129.315789 | 3 | 886.699115 | 0 | 1216.421053 | 0 | 1517.424779 | 0 |
1143.245614 | 0 | 897.6460177 | 0 | 1231.438596 | 0 | 1535.911504 | 0 |
1157.175439 | 3 | 908.5929204 | 0 | 1246.45614 | 0 | 1554.39823 | 0 |
1171.105263 | 3 | 919.539823 | 0 | 1261.473684 | 0 | 1572.884956 | 0 |
1185.035088 | 2 | 930.4867257 | 0 | 1276.491228 | 0 | 1591.371681 | 0 |
1198.964912 | 2 | 941.4336283 | 0 | 1291.508772 | 0 | 1609.858407 | 0 |
1212.894737 | 2 | 952.380531 | 0 | 1306.526316 | 0 | 1628.345133 | 0 |
1226.824561 | 4 | 963.3274336 | 0 | 1321.54386 | 0 | 1646.831858 | 0 |
1240.754386 | 7 | 974.2743363 | 0 | 1336.561404 | 0 | 1665.318584 | 0 |
1254.684211 | 2 | 985.2212389 | 0 | 1351.578947 | 0 | 1683.80531 | 0 |
1268.614035 | 2 | 996.1681416 | 0 | 1366.596491 | 0 | 1702.292035 | 0 |
1282.54386 | 4 | 1007.115044 | 0 | 1381.614035 | 0 | 1720.778761 | 0 |
1296.473684 | 2 | 1018.061947 | 0 | 1396.631579 | 0 | 1739.265487 | 0 |
1310.403509 | 0 | 1029.00885 | 0 | 1411.649123 | 0 | 1757.752212 | 0 |
1324.333333 | 1 | 1039.955752 | 0 | 1426.666667 | 0 | 1776.238938 | 0 |
1338.263158 | 1 | 1050.902655 | 0 | 1441.684211 | 0 | 1794.725664 | 0 |
1352.192982 | 0 | 1061.849558 | 0 | 1456.701754 | 0 | 1813.212389 | 0 |
1366.122807 | 1 | 1072.79646 | 0 | 1471.719298 | 0 | 1831.699115 | 0 |
1380.052632 | 1 | 1083.743363 | 0 | 1486.736842 | 0 | 1850.185841 | 0 |
1393.982456 | 2 | 1094.690265 | 0 | 1501.754386 | 0 | 1868.672566 | 0 |
1407.912281 | 0 | 1105.637168 | 0 | 1516.77193 | 0 | 1887.159292 | 0 |
1421.842105 | 2 | 1116.584071 | 0 | 1531.789474 | 0 | 1905.646018 | 0 |
1435.77193 | 1 | 1127.530973 | 0 | 1546.807018 | 0 | 1924.132743 | 0 |
1449.701754 | 0 | 1138.477876 | 0 | 1561.824561 | 0 | 1942.619469 | 0 |
1463.631579 | 1 | 1149.424779 | 0 | 1576.842105 | 0 | 1961.106195 | 0 |
1477.561404 | 1 | 1160.371681 | 0 | 1591.859649 | 0 | 1979.59292 | 0 |
1491.491228 | 0 | 1171.318584 | 0 | 1606.877193 | 0 | 1998.079646 | 0 |
1505.421053 | 0 | 1182.265487 | 0 | 1621.894737 | 0 | 2016.566372 | 0 |
1519.350877 | 0 | 1193.212389 | 0 | 1636.912281 | 0 | 2035.053097 | 0 |
1533.280702 | 0 | 1204.159292 | 0 | 1651.929825 | 0 | 2053.539823 | 0 |
1547.210526 | 0 | 1215.106195 | 0 | 1666.947368 | 0 | 2072.026549 | 0 |
1561.140351 | 1 | 1226.053097 | 0 | 1681.964912 | 0 | 2090.513274 | 0 |
1575.070175 | 0 | More | 1 | 1696.982456 | 0 | More | 1 |
More | 1 | More | 1 |