BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081915.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 = 2,763,553 number of mapped reads = 2,550,000 (92.27%) number of supplementary alignments = 19,391 (0.7%) number of secondary alignments = 0 number of mapped bases = 174,084,506 bp number of sequenced bases = 174,016,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,797 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1503 >>>>>>> ACTG content number of A's = 49,100,162 bp (28.22%) number of C's = 32,880,513 bp (18.9%) number of T's = 54,077,085 bp (31.08%) number of G's = 37,956,321 bp (21.81%) number of N's = 2,097 bp (0%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,496,594 number of insertions = 14,450 mapped reads with insertion percentage = 0.56% number of deletions = 41,177 mapped reads with deletion percentage = 1.6% homopolymer indels = 47.08% >>>>>>> Coverage mean coverageData = 0.0562X std coverageData = 0.4635X There is a 4.81% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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% 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 14272373 0.057261133162833724 0.875890469073002 chr2 243199373 15491700 0.06369958856760703 0.5491296528469174 chr3 198022430 11586105 0.0585090537470932 0.27695511474127466 chr4 191154276 11001776 0.05755443315325052 0.3024691043825661 chr5 180915260 10835710 0.059893842012000535 0.2770920131008026 chr6 171115067 10004069 0.05846398669265051 0.31580857991777417 chr7 159138663 10076591 0.06331956552883695 0.6000612993228982 chr8 146364022 8467659 0.05785341837627282 0.5805202000952437 chr9 141213431 7692395 0.054473536585907326 0.44830827491775893 chr10 135534747 8231136 0.060730817610926004 0.49517241186529176 chr11 135006516 7485549 0.05544583492547871 0.3531922116967552 chr12 133851895 7975257 0.05958269772721559 0.2782257440636369 chr13 115169878 5910206 0.05131728975175263 0.25338741026454115 chr14 107349540 5645312 0.05258813405255393 0.28020933673833726 chr15 102531392 5198693 0.0507034274927234 0.2717968763695467 chr16 90354753 4986126 0.05518388169352862 0.3214784971671171 chr17 81195210 4767710 0.058719104242725646 0.30126896012178195 chr18 78077248 4630448 0.05930598373549232 0.8162033129352174 chr19 59128983 3206356 0.05422646961474037 0.612381451754742 chr20 63025520 3519285 0.055839047420790815 0.27547077977334383 chr21 48129895 2247921 0.04670529615740903 0.2687963160659906 chr22 51304566 1898354 0.03700165790311919 0.21609257165734044 chrMT 16571 14412 0.8697121477279585 1.0380035878493652 chrX 155270560 8508771 0.05479964134862397 0.3033577637826393 chrY 59373566 430592 0.007252250942784875 0.18274491471341325