BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230338.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 = 3,257,585 number of mapped reads = 2,768,033 (84.97%) number of supplementary alignments = 19,837 (0.61%) number of secondary alignments = 0 number of mapped bases = 183,384,144 bp number of sequenced bases = 183,306,472 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,105 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2797 >>>>>>> ACTG content number of A's = 50,354,500 bp (27.47%) number of C's = 31,949,914 bp (17.43%) number of T's = 60,808,294 bp (33.17%) number of G's = 39,836,286 bp (21.73%) number of N's = 357,478 bp (0.2%) GC percentage = 39.16% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,837,134 number of insertions = 16,762 mapped reads with insertion percentage = 0.6% number of deletions = 47,312 mapped reads with deletion percentage = 1.69% homopolymer indels = 48.61% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.5521X There is a 4.96% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15234265 0.06112026898420446 1.1408654208847266 chr2 243199373 14122988 0.05807164642648976 0.5039834428560473 chr3 198022430 11345487 0.0572939489733562 0.2741122535482441 chr4 191154276 11160292 0.05838369004102215 0.3136115725658212 chr5 180915260 12707324 0.07023909425882592 0.3090075379574705 chr6 171115067 10975584 0.06414154049917767 0.4002640159821256 chr7 159138663 11929375 0.07496214166383941 0.8059539499851314 chr8 146364022 9533955 0.06513865135518071 0.9173979614965785 chr9 141213431 8222674 0.058228696390784526 0.48141424503354047 chr10 135534747 10188748 0.07517443478903606 0.47238154849598235 chr11 135006516 6112961 0.045279007125848654 0.37686145478036637 chr12 133851895 9955524 0.07437716141411371 0.32117784712652836 chr13 115169878 5255184 0.04562984776279784 0.24354799075352904 chr14 107349540 6345467 0.05911033247091697 0.309417606693931 chr15 102531392 5615638 0.05476993816683967 0.2681537231538091 chr16 90354753 3890892 0.04306239429374568 0.2791216640384215 chr17 81195210 4296832 0.05291977199147585 0.29958180298944276 chr18 78077248 5999357 0.07683873540214942 0.8851299861615594 chr19 59128983 3664620 0.061976712841484184 0.6720559608037587 chr20 63025520 4026290 0.06388348719693229 0.31219241287309707 chr21 48129895 2804508 0.05826956406200346 0.3179719892502211 chr22 51304566 1752173 0.0341523793418309 0.2092034819845226 chrMT 16571 117583 7.095709371794098 4.212135341604052 chrX 155270560 7667144 0.04937925128884703 0.28994865896953187 chrY 59373566 459279 0.00773541208557357 0.17729335070888286