BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013213.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 = 1,397,851 number of mapped reads = 53,719 (3.84%) number of supplementary alignments = 533 (0.04%) number of secondary alignments = 0 number of mapped bases = 3,351,239 bp number of sequenced bases = 3,349,946 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,244 duplication rate = 8.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9986 >>>>>>> ACTG content number of A's = 916,248 bp (27.35%) number of C's = 603,361 bp (18.01%) number of T's = 1,081,459 bp (32.28%) number of G's = 748,534 bp (22.34%) number of N's = 344 bp (0.01%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 39,395 number of insertions = 274 mapped reads with insertion percentage = 0.51% number of deletions = 763 mapped reads with deletion percentage = 1.41% homopolymer indels = 44.55% >>>>>>> Coverage mean coverageData = 0.0011X std coverageData = 0.0868X There is a 0.06% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 242052 9.711189445742645E-4 0.06727381818289617 chr2 243199373 278933 0.001146931410879912 0.07049246856691191 chr3 198022430 255233 0.0012889095442369836 0.08352921526237346 chr4 191154276 242230 0.0012671963456365475 0.07328630762799755 chr5 180915260 225681 0.0012474403762291805 0.08012289126411405 chr6 171115067 198395 0.0011594244941621652 0.09518963862190846 chr7 159138663 186312 0.0011707525782091055 0.08054681062806301 chr8 146364022 180938 0.0012362191030798539 0.0709585818712687 chr9 141213431 125198 8.865870555896343E-4 0.05613601007854444 chr10 135534747 147748 0.001090111600680525 0.062156558130395986 chr11 135006516 135275 0.0010019886743836868 0.06847519408691397 chr12 133851895 176959 0.0013220507636443996 0.08821584599803749 chr13 115169878 108663 9.435019111507611E-4 0.07925415938488027 chr14 107349540 116006 0.0010806380725991 0.07822593567981001 chr15 102531392 69944 6.821715636124398E-4 0.05930244471071566 chr16 90354753 78852 8.726934376103048E-4 0.055584292045605915 chr17 81195210 93062 0.0011461513554802062 0.06864917494167411 chr18 78077248 113810 0.0014576589584714872 0.3136267174848128 chr19 59128983 46547 7.872112395371319E-4 0.04788451029510697 chr20 63025520 72983 0.0011579912391044135 0.06196024862804851 chr21 48129895 35799 7.437996696232145E-4 0.04309803243104761 chr22 51304566 34510 6.72649681901607E-4 0.04910163995799486 chrMT 16571 1616 0.09751976344215799 0.33653824350091105 chrX 155270560 173296 0.0011160905196709538 0.06966425004374997 chrY 59373566 11197 1.8858560727176132E-4 0.02545677623184091