BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1298935.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 167,952,506 number of mapped reads = 139,472,246 (83.04%) number of supplementary alignments = 907,198 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 74,275,816 number of mapped paired reads (second in pair) = 65,196,430 number of mapped paired reads (both in pair) = 127,571,580 number of mapped paired reads (singletons) = 11,900,666 number of mapped bases = 11,382,680,237 bp number of sequenced bases = 11,371,959,500 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,996,358 duplication rate = 53.23% >>>>>>> Insert size mean insert size = 548,997.4284 std insert size = 7,246,271.1849 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 51.6301 >>>>>>> ACTG content number of A's = 3,457,702,498 bp (30.41%) number of C's = 2,315,465,480 bp (20.36%) number of T's = 3,291,177,845 bp (28.94%) number of G's = 2,305,196,824 bp (20.27%) number of N's = 2,416,853 bp (0.02%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0137 number of mismatches = 122,525,697 number of insertions = 9,359,539 mapped reads with insertion percentage = 6.48% number of deletions = 3,809,079 mapped reads with deletion percentage = 2.67% homopolymer indels = 49.53% >>>>>>> Coverage mean coverageData = 3.6769X std coverageData = 514.1652X There is a 6.93% of reference with a coverageData >= 1X There is a 3.63% of reference with a coverageData >= 2X There is a 2.46% of reference with a coverageData >= 3X There is a 1.92% of reference with a coverageData >= 4X There is a 1.61% of reference with a coverageData >= 5X There is a 1.4% of reference with a coverageData >= 6X There is a 1.24% of reference with a coverageData >= 7X There is a 1.12% of reference with a coverageData >= 8X There is a 1.01% of reference with a coverageData >= 9X There is a 0.91% of reference with a coverageData >= 10X There is a 0.82% of reference with a coverageData >= 11X There is a 0.74% of reference with a coverageData >= 12X There is a 0.67% of reference with a coverageData >= 13X There is a 0.61% of reference with a coverageData >= 14X There is a 0.56% of reference with a coverageData >= 15X There is a 0.51% of reference with a coverageData >= 16X There is a 0.46% of reference with a coverageData >= 17X There is a 0.43% of reference with a coverageData >= 18X There is a 0.39% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.32% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1052463677 4.222511754544435 576.1106250138494 chr2 243199373 519943228 2.1379299690875437 266.0847460700983 chr3 198022430 516712499 2.6093634897824454 318.3214932169887 chr4 191154276 681739731 3.566437253017557 525.9369888333664 chr5 180915260 728109331 4.024587704762992 587.6305952378007 chr6 171115067 421016537 2.4604293729435294 383.3329673293693 chr7 159138663 555076850 3.488007499472331 437.9078644266984 chr8 146364022 537219330 3.6704329565362723 460.78351833938393 chr9 141213431 359929669 2.548834529769339 308.597258562362 chr10 135534747 546386436 4.031338443417761 487.6404086303968 chr11 135006516 482739320 3.575674228938698 407.7947471612218 chr12 133851895 628116529 4.692623358077971 632.6783875647809 chr13 115169878 152382190 1.3231080265622925 241.26094010301924 chr14 107349540 304092994 2.8327368147082885 337.88928660137134 chr15 102531392 683585055 6.667080604933171 810.7348856923096 chr16 90354753 452931510 5.012813327042132 628.3991465687461 chr17 81195210 313304154 3.858653164392333 319.5884753689168 chr18 78077248 216622686 2.77446620557118 300.35536855173757 chr19 59128983 516884552 8.741644550186159 790.687762113535 chr20 63025520 399737392 6.342468765033593 677.06663434873 chr21 48129895 251958983 5.234978862929163 693.4979212833721 chr22 51304566 136468811 2.6599739875004498 327.8682738878341 chrMT 16571 684082 41.28187797960292 30.766693027574505 chrX 155270560 724619408 4.666817766355709 589.2250527540956 chrY 59373566 199955283 3.3677492606726704 1222.877786933006