BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472562.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 12,155,966 number of mapped reads = 11,974,778 (98.51%) number of supplementary alignments = 42,262 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,013,537 number of mapped paired reads (second in pair) = 5,961,241 number of mapped paired reads (both in pair) = 11,879,180 number of mapped paired reads (singletons) = 95,598 number of mapped bases = 1,176,803,398 bp number of sequenced bases = 1,176,666,343 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,213,633 duplication rate = 45.39% >>>>>>> Insert size mean insert size = 29,761.8466 std insert size = 1,725,838.8631 median insert size = 249 >>>>>>> Mapping quality mean mapping quality = 54.1129 >>>>>>> ACTG content number of A's = 318,897,276 bp (27.1%) number of C's = 271,818,470 bp (23.1%) number of T's = 315,969,904 bp (26.85%) number of G's = 269,802,094 bp (22.93%) number of N's = 178,599 bp (0.02%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 7,646,551 number of insertions = 67,909 mapped reads with insertion percentage = 0.56% number of deletions = 55,248 mapped reads with deletion percentage = 0.46% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.3801X std coverageData = 13.9244X There is a 3.68% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.15% 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 0.14% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 140055291 0.5619054846808185 17.94132829853535 chr2 243199373 84227766 0.34633216755867213 10.645033926474444 chr3 198022430 93537456 0.4723578839023438 12.496475726155227 chr4 191154276 47115359 0.24647818498185203 9.942777578112674 chr5 180915260 57484685 0.31774370498099497 10.158767642275851 chr6 171115067 125549727 0.7337152081411977 21.030835302530292 chr7 159138663 44265238 0.2781551457423015 8.515597078368636 chr8 146364022 95462136 0.6522240554444452 21.544624549614152 chr9 141213431 26987455 0.19111110613833893 7.637322162580207 chr10 135534747 27350225 0.20179493159787285 6.609152860476234 chr11 135006516 14514867 0.10751234407085951 3.2598510791662716 chr12 133851895 55088381 0.41156220462922843 26.4249658065845 chr13 115169878 22324205 0.19383718544878548 8.155778593355326 chr14 107349540 6017452 0.05605475347169629 5.658830199759876 chr15 102531392 13956750 0.13612172552967974 4.803016406529326 chr16 90354753 57919227 0.64102025711918 16.838688774615484 chr17 81195210 72732332 0.8957712160606519 18.41837909351316 chr18 78077248 700467 0.008971461186746747 0.7236969507646822 chr19 59128983 22910498 0.38746646462700024 9.767637242561811 chr20 63025520 67546178 1.0717274208923624 25.903397164241415 chr21 48129895 7197004 0.14953292543023416 6.442777967981388 chr22 51304566 14183344 0.276453834537846 9.831542328354367 chrMT 16571 3109 0.18761692112727052 0.5391945232898491 chrX 155270560 79422400 0.5115097156859614 15.641016815539166 chrY 59373566 251846 0.004241719286323479 0.27052204802404206