BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524590.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 = 1,445,513 number of mapped reads = 1,351,269 (93.48%) number of supplementary alignments = 3,003 (0.21%) number of secondary alignments = 0 number of mapped bases = 79,637,142 bp number of sequenced bases = 79,611,961 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,253 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5823 >>>>>>> ACTG content number of A's = 20,110,851 bp (25.26%) number of C's = 14,805,579 bp (18.6%) number of T's = 25,511,587 bp (32.04%) number of G's = 19,183,423 bp (24.1%) number of N's = 521 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 365,661 number of insertions = 6,033 mapped reads with insertion percentage = 0.44% number of deletions = 14,745 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.22% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.2382X There is a 2.29% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 7483277 0.03002310273080523 0.4068125019805407 chr2 243199373 6979091 0.028696994214701368 0.2682995738155696 chr3 198022430 4358966 0.02201248616128991 0.16340791027479992 chr4 191154276 3517621 0.018402000068259 0.16475349480136633 chr5 180915260 4980225 0.027527943192851727 0.18142483803730813 chr6 171115067 5264869 0.030768003614783962 0.20631559610222885 chr7 159138663 4575615 0.028752378044045776 0.2998335756586135 chr8 146364022 7544255 0.051544463570425796 0.3315029279757579 chr9 141213431 2859727 0.02025109778686703 0.20396653550420443 chr10 135534747 3413364 0.025184420051339307 0.23554636338909665 chr11 135006516 6081267 0.04504424808651458 0.26846377174085473 chr12 133851895 2651328 0.01980792277912838 0.16076862444328927 chr13 115169878 1956821 0.016990736067290096 0.14503933164763327 chr14 107349540 1431259 0.013332698025534157 0.13100166061411264 chr15 102531392 1980891 0.019319848890767034 0.15767044496149518 chr16 90354753 2312604 0.02559471331851242 0.18139988918949462 chr17 81195210 1664989 0.02050600029238178 0.1618716916695225 chr18 78077248 1815328 0.02325040964558587 0.3234547956068742 chr19 59128983 1583550 0.026781282539562704 0.30920538278418686 chr20 63025520 1169593 0.018557451013494215 0.151850861075394 chr21 48129895 725388 0.01507146441935932 0.1455479368113707 chr22 51304566 1385396 0.027003366522971854 0.17930356811520118 chrMT 16571 3373 0.20354836763019732 0.5590926063155396 chrX 155270560 3710863 0.023899334168692377 0.18917735514866282 chrY 59373566 187482 0.0031576678416115347 0.09059991021692954