BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231768.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,057,036 number of mapped reads = 628,014 (59.41%) number of supplementary alignments = 3,088 (0.29%) number of secondary alignments = 0 number of mapped bases = 39,456,477 bp number of sequenced bases = 39,432,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,878 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0447 >>>>>>> ACTG content number of A's = 11,103,268 bp (28.16%) number of C's = 6,429,604 bp (16.31%) number of T's = 12,788,126 bp (32.43%) number of G's = 9,110,518 bp (23.1%) number of N's = 736 bp (0%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 424,598 number of insertions = 3,082 mapped reads with insertion percentage = 0.49% number of deletions = 14,333 mapped reads with deletion percentage = 2.25% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 0.1597X There is a 1.19% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4316393 0.017317481427659112 0.24904486583270063 chr2 243199373 2619140 0.010769517896742275 0.13365903014670896 chr3 198022430 2957258 0.014933954704020145 0.12861181428040955 chr4 191154276 1693204 0.008857787727437496 0.09975366223480527 chr5 180915260 2122851 0.011733952127642522 0.11807469208188993 chr6 171115067 3042041 0.017777750687494983 0.15283984813507798 chr7 159138663 2405636 0.015116603059559449 0.16925241274745842 chr8 146364022 1975899 0.013499895486610774 0.3543349367390909 chr9 141213431 1345760 0.009529971692281876 0.1136440462351891 chr10 135534747 1430525 0.010554673481627556 0.12131094845073868 chr11 135006516 1659841 0.012294525102773558 0.12874310704808697 chr12 133851895 1323784 0.00988991601501047 0.10480651567941598 chr13 115169878 2081483 0.018073154510070768 0.14291126844886 chr14 107349540 2101820 0.019579217572800033 0.1506501251366672 chr15 102531392 658232 0.006419809456990499 0.08435805366931931 chr16 90354753 1107441 0.012256588206267356 0.12067900081616681 chr17 81195210 1018907 0.012548856022418071 0.12042303355453736 chr18 78077248 807689 0.010344742171240462 0.19050502345718295 chr19 59128983 970774 0.016417904566361306 0.16746618105637565 chr20 63025520 895541 0.014209180662055624 0.12713418755680456 chr21 48129895 878958 0.018262204810544466 0.14381874756294113 chr22 51304566 331485 0.006461120828894645 0.08414741825191717 chrMT 16571 27109 1.6359302395751614 1.6336942667904732 chrX 155270560 1596661 0.010283089080119245 0.11074292589996902 chrY 59373566 88045 0.001482898972246336 0.044161314948316314