BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231871.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 = 4,146,513 number of mapped reads = 3,913,671 (94.38%) number of supplementary alignments = 27,137 (0.65%) number of secondary alignments = 0 number of mapped bases = 254,772,964 bp number of sequenced bases = 254,671,344 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 438,338 duplication rate = 9.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0641 >>>>>>> ACTG content number of A's = 68,060,193 bp (26.72%) number of C's = 45,376,561 bp (17.82%) number of T's = 83,351,531 bp (32.73%) number of G's = 57,783,392 bp (22.69%) number of N's = 99,667 bp (0.04%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,540,527 number of insertions = 16,704 mapped reads with insertion percentage = 0.42% number of deletions = 57,380 mapped reads with deletion percentage = 1.45% homopolymer indels = 44.94% >>>>>>> Coverage mean coverageData = 0.0823X std coverageData = 0.7204X There is a 5.97% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 38061075 0.15270202676847092 1.3727751991790382 chr2 243199373 20784881 0.08546436918651101 1.025802225057574 chr3 198022430 20710131 0.10458477355317779 0.42182526662415976 chr4 191154276 12069143 0.0631382318646118 0.3570852005443593 chr5 180915260 15276899 0.08444229082720828 0.38527514208149527 chr6 171115067 11360869 0.0663931540289202 0.4447990635205476 chr7 159138663 9245860 0.05809939473979368 0.7279085983168245 chr8 146364022 9748118 0.06660187296574838 1.1764845697506439 chr9 141213431 10123262 0.07168767112527703 0.5623244487922386 chr10 135534747 14152446 0.1044193191285479 0.6741002828396552 chr11 135006516 9738749 0.07213539974618706 0.44567604862353194 chr12 133851895 6278431 0.046905805853551794 0.31202961266202794 chr13 115169878 19163061 0.16638952244092853 0.5518736614683598 chr14 107349540 6101384 0.05683661057140999 0.37704808877891377 chr15 102531392 7482731 0.07297990258437143 0.3809415686460326 chr16 90354753 5699722 0.06308159571860043 0.41551387361240916 chr17 81195210 9770516 0.12033365022394794 0.5158012732989272 chr18 78077248 7712494 0.09878030024828743 1.3005695264194983 chr19 59128983 6167427 0.10430463517358315 0.9244711970058229 chr20 63025520 4623685 0.07336210792072799 0.4133423555694233 chr21 48129895 2832854 0.05885851194979752 0.333943663611728 chr22 51304566 1749285 0.03409608805578825 0.2328294364751186 chrMT 16571 153020 9.234204332870677 6.005977191065472 chrX 155270560 5281108 0.03401229441047936 0.3211609982659951 chrY 59373566 485813 0.00818231129994786 0.18887040780493633