BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524890.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 = 2,085,159 number of mapped reads = 1,921,612 (92.16%) number of supplementary alignments = 7,646 (0.37%) number of secondary alignments = 0 number of mapped bases = 112,161,550 bp number of sequenced bases = 112,128,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,288 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0458 >>>>>>> ACTG content number of A's = 28,182,088 bp (25.13%) number of C's = 19,710,703 bp (17.58%) number of T's = 37,125,312 bp (33.11%) number of G's = 27,095,372 bp (24.16%) number of N's = 14,594 bp (0.01%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 549,839 number of insertions = 9,005 mapped reads with insertion percentage = 0.47% number of deletions = 21,093 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.3504X There is a 3.23% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9045011 0.03628882031952891 0.7067619755488818 chr2 243199373 9495186 0.039042806249340124 0.3751968745568606 chr3 198022430 7430154 0.03752177972970032 0.21327038253367167 chr4 191154276 7245266 0.03790271476846273 0.24284761033927163 chr5 180915260 6803323 0.03760502568992798 0.21319801813566716 chr6 171115067 6506050 0.0380214911174362 0.2404987331455683 chr7 159138663 6126187 0.03849590592576488 0.4786058388856448 chr8 146364022 5798854 0.0396193949903891 0.3277144482850973 chr9 141213431 4654019 0.03295733958903668 0.3022043019346951 chr10 135534747 5419113 0.03998320076548341 0.33959333816216597 chr11 135006516 5164616 0.03825456839431365 0.31413536639870127 chr12 133851895 5045526 0.03769484175027929 0.22055943061340402 chr13 115169878 3506813 0.030449046755089904 0.19204413976926157 chr14 107349540 3416829 0.03182900457701077 0.2107239870499238 chr15 102531392 3172615 0.030942864795983654 0.19330424021091488 chr16 90354753 3204154 0.03546193081840421 0.23236483424802354 chr17 81195210 2956124 0.03640761567092443 0.23392008832960495 chr18 78077248 3033346 0.03885057526617741 0.6047040182873982 chr19 59128983 2162383 0.03657061038915552 0.4615715091037142 chr20 63025520 2369331 0.037593200341702854 0.21699150674756285 chr21 48129895 1462587 0.030388327254817406 0.21868393721214585 chr22 51304566 1308824 0.025510867785140216 0.1740888341538425 chrMT 16571 10145 0.6122141089855773 0.9891722002178103 chrX 155270560 6479733 0.04173188400943489 0.2629723950359595 chrY 59373566 345361 0.005816746799409017 0.1566905792501109