BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231848.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 = 8,167,022 number of mapped reads = 5,678,421 (69.53%) number of supplementary alignments = 40,325 (0.49%) number of secondary alignments = 0 number of mapped bases = 365,047,515 bp number of sequenced bases = 364,908,002 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 378,681 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1344 >>>>>>> ACTG content number of A's = 104,525,541 bp (28.64%) number of C's = 74,903,943 bp (20.53%) number of T's = 100,236,718 bp (27.47%) number of G's = 85,213,974 bp (23.35%) number of N's = 27,826 bp (0.01%) GC percentage = 43.88% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 2,313,650 number of insertions = 26,893 mapped reads with insertion percentage = 0.47% number of deletions = 83,904 mapped reads with deletion percentage = 1.46% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 0.1179X std coverageData = 13.8224X There is a 8.97% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.11% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 31443609 0.1261525803781247 2.7139268788293793 chr2 243199373 30080358 0.12368600144376195 49.15074931556638 chr3 198022430 35823858 0.18090808197839003 0.5240191216902248 chr4 191154276 11953491 0.06253321270197482 0.3674758376690418 chr5 180915260 22368364 0.12364000692921094 0.45555841002922975 chr6 171115067 23296015 0.13614239475475295 0.7519838648929021 chr7 159138663 24933162 0.15667570362835084 1.8879714069714397 chr8 146364022 23475468 0.1603909736779439 1.0687608070661536 chr9 141213431 13298834 0.09417541876735507 0.8984356720363672 chr10 135534747 16123415 0.11896148668060745 0.9071160540831688 chr11 135006516 15533422 0.11505683177543816 0.9881183382171158 chr12 133851895 12246936 0.0914961719443718 0.40736049030424204 chr13 115169878 14732781 0.12792217249722188 0.44157517434180726 chr14 107349540 16064611 0.14964769294772945 0.7023960177946402 chr15 102531392 7357443 0.07175795487103111 0.35301898893897116 chr16 90354753 10532296 0.11656604274044112 0.6040881193588277 chr17 81195210 8912621 0.10976781758431316 0.5384507739338908 chr18 78077248 7971094 0.1020924046913129 2.287244539689103 chr19 59128983 10120722 0.1711634715584403 1.5366551649065838 chr20 63025520 8476507 0.13449324971852672 0.5199630434302226 chr21 48129895 5924668 0.12309746364499652 0.47151989440235165 chr22 51304566 2878545 0.05610699445347613 0.28140747464792454 chrMT 16571 209865 12.664594774002776 8.01797382333128 chrX 155270560 10576864 0.06811892737425562 0.5209913764714891 chrY 59373566 712566 0.012001401431741526 0.21308591075429698