BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080638.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,211,473 number of mapped reads = 2,597,276 (80.87%) number of supplementary alignments = 29,680 (0.92%) number of secondary alignments = 0 number of mapped bases = 173,528,209 bp number of sequenced bases = 173,463,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,972 duplication rate = 5.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7851 >>>>>>> ACTG content number of A's = 48,243,899 bp (27.81%) number of C's = 31,083,986 bp (17.92%) number of T's = 56,349,402 bp (32.48%) number of G's = 37,642,079 bp (21.7%) number of N's = 144,374 bp (0.08%) GC percentage = 39.62% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,550,038 number of insertions = 13,653 mapped reads with insertion percentage = 0.52% number of deletions = 39,916 mapped reads with deletion percentage = 1.52% homopolymer indels = 49.55% >>>>>>> Coverage mean coverageData = 0.0561X std coverageData = 0.3655X There is a 4.2% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 23629614 0.09480262839545744 0.5343347603461727 chr2 243199373 12342546 0.05075073117067617 0.35464081788046437 chr3 198022430 10981861 0.05545766204363819 0.2978470525590557 chr4 191154276 8106431 0.0424077931691154 0.26160071781857136 chr5 180915260 8294349 0.04584659690951443 0.2698718764464877 chr6 171115067 10342907 0.06044416299121105 0.40717669982951554 chr7 159138663 10509785 0.0660416821523755 0.5908532860576893 chr8 146364022 19551240 0.1335795486680463 0.585867209807059 chr9 141213431 5608795 0.03971856614687026 0.2824059937846477 chr10 135534747 7431406 0.05483026430115371 0.3337044469912746 chr11 135006516 6075169 0.044999079896262194 0.2749762998982145 chr12 133851895 5009622 0.037426604980078916 0.24570471722260315 chr13 115169878 4068770 0.03532842155133654 0.23698124868653933 chr14 107349540 2991884 0.027870487381687896 0.21687924824183857 chr15 102531392 3426573 0.03341974524251071 0.23311718009848292 chr16 90354753 4654867 0.0515176772161615 0.2953111373777807 chr17 81195210 2841661 0.03499788965383549 0.23680684012350456 chr18 78077248 5698181 0.07298132485407273 0.4343830492731657 chr19 59128983 3076486 0.05203008480629542 0.3931911475426068 chr20 63025520 4247444 0.06739244674220855 0.33452505690076184 chr21 48129895 3149882 0.06544543677063912 0.33348923857378066 chr22 51304566 1456057 0.028380651343975896 0.20828036534923108 chrMT 16571 50368 3.0395268843159737 5.820627915231265 chrX 155270560 9686886 0.06238713893992525 0.3400381105915261 chrY 59373566 295425 0.004975699118358497 0.09315634117321267