BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867843.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,317,177 number of mapped reads = 1,217,081 (92.4%) number of supplementary alignments = 5,645 (0.43%) number of secondary alignments = 0 number of mapped bases = 71,933,763 bp number of sequenced bases = 71,912,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,020 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9312 >>>>>>> ACTG content number of A's = 17,423,111 bp (24.23%) number of C's = 12,965,842 bp (18.03%) number of T's = 23,561,662 bp (32.76%) number of G's = 17,951,748 bp (24.96%) number of N's = 9,775 bp (0.01%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 364,318 number of insertions = 5,198 mapped reads with insertion percentage = 0.43% number of deletions = 13,446 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.28% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2356X There is a 2.12% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5832228 0.023399051029846782 0.41226810269368724 chr2 243199373 6045326 0.024857490072558698 0.31310990881030853 chr3 198022430 4726622 0.023869124320916577 0.16503614911460535 chr4 191154276 4633923 0.024241796191888484 0.1861596127657431 chr5 180915260 4322561 0.023892738511942 0.1667413425386084 chr6 171115067 4138807 0.02418727393538057 0.18588294580147816 chr7 159138663 4007949 0.025185262490234697 0.2741737700427395 chr8 146364022 3722375 0.025432308767792674 0.2480352098643912 chr9 141213431 3009481 0.02131157765014576 0.19413613137954427 chr10 135534747 3430730 0.02531254955601902 0.241423375852303 chr11 135006516 3135846 0.023227367781270648 0.20150747701861946 chr12 133851895 3254198 0.02431193073508597 0.1692661563483529 chr13 115169878 2232956 0.019388368198149868 0.14901029127563137 chr14 107349540 2231443 0.020786702951871055 0.15950050141612604 chr15 102531392 2058794 0.02007964546116764 0.1534739250298242 chr16 90354753 2154314 0.02384284089626143 0.17603095891499712 chr17 81195210 1975985 0.024336226237976353 0.17514529752167232 chr18 78077248 1932081 0.024745762043252344 0.33555562627477775 chr19 59128983 1519530 0.02569856477998277 0.3314548969268954 chr20 63025520 1533561 0.024332381549569126 0.16981738196959983 chr21 48129895 928013 0.01928142581653253 0.1685728317917748 chr22 51304566 864676 0.01685378256586363 0.13919399778654473 chrMT 16571 14168 0.8549876289904049 1.0699548061560633 chrX 155270560 3990399 0.025699649695344693 0.18565758884080422 chrY 59373566 237797 0.004005098834723856 0.15073519550985534