BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008711.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 = 1,474,527 number of mapped reads = 1,153,036 (78.2%) number of supplementary alignments = 4,126 (0.28%) number of secondary alignments = 0 number of mapped bases = 78,346,997 bp number of sequenced bases = 78,310,491 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,003 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1801 >>>>>>> ACTG content number of A's = 23,919,528 bp (30.54%) number of C's = 13,469,888 bp (17.2%) number of T's = 23,300,993 bp (29.75%) number of G's = 17,616,132 bp (22.5%) number of N's = 3,950 bp (0.01%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 660,927 number of insertions = 5,733 mapped reads with insertion percentage = 0.49% number of deletions = 22,707 mapped reads with deletion percentage = 1.94% homopolymer indels = 47.53% >>>>>>> Coverage mean coverageData = 0.0253X std coverageData = 0.1982X There is a 2.35% of reference with a coverageData >= 1X There is a 0.14% 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 4845778 0.019441387871206146 0.23135190438437594 chr2 243199373 7048332 0.02898170300792675 0.26429854306745126 chr3 198022430 6595822 0.03330845904678576 0.19219824503825134 chr4 191154276 3627925 0.018979041829019824 0.14693726704219226 chr5 180915260 4235681 0.023412513681819874 0.1602733743674341 chr6 171115067 3574882 0.020891684541139793 0.16019599982085417 chr7 159138663 4541244 0.02853639658892949 0.21090787089407562 chr8 146364022 7346434 0.050192895081825506 0.3092467919798275 chr9 141213431 2788771 0.019748624335882044 0.1693334864833028 chr10 135534747 4593699 0.033893146235038904 0.22641125942659535 chr11 135006516 3949013 0.02925053632226166 0.20692493553444635 chr12 133851895 3589308 0.026815518749286293 0.1717823893436067 chr13 115169878 2534464 0.02200630967065885 0.1550995872804041 chr14 107349540 3138346 0.029234834168828296 0.18488641859455218 chr15 102531392 2417457 0.0235777253467894 0.1630506151367364 chr16 90354753 2229214 0.024671795627619057 0.17602956172658168 chr17 81195210 1830052 0.02253891578086934 0.16409358956486958 chr18 78077248 1424766 0.018248158541653518 0.24456042499557779 chr19 59128983 1355414 0.022923005457408257 0.1907202993247274 chr20 63025520 1837130 0.02914898599805285 0.18046769530488874 chr21 48129895 785561 0.016321685305982905 0.14046434844564176 chr22 51304566 994779 0.01938967771406545 0.14616594423397455 chrMT 16571 16766 1.0117675457123891 1.1981590763717012 chrX 155270560 2892942 0.018631619542043256 0.14887518923487075 chrY 59373566 153217 0.0025805591666837055 0.06940093351603295