BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173892.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,355,070 number of mapped reads = 2,296,145 (97.5%) number of supplementary alignments = 236,894 (10.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,149,278 number of mapped paired reads (second in pair) = 1,146,867 number of mapped paired reads (both in pair) = 2,255,212 number of mapped paired reads (singletons) = 40,933 number of mapped bases = 272,624,060 bp number of sequenced bases = 272,478,624 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,795,565 duplication rate = 64.17% >>>>>>> Insert size mean insert size = 1,261,038.3344 std insert size = 10,634,607.2607 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 52.6688 >>>>>>> ACTG content number of A's = 82,098,370 bp (30.13%) number of C's = 53,189,089 bp (19.52%) number of T's = 81,945,935 bp (30.07%) number of G's = 55,242,360 bp (20.27%) number of N's = 2,870 bp (0%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 2,798,925 number of insertions = 28,455 mapped reads with insertion percentage = 1.2% number of deletions = 59,388 mapped reads with deletion percentage = 2.53% homopolymer indels = 42.63% >>>>>>> Coverage mean coverageData = 0.0881X std coverageData = 1.4309X There is a 1.88% of reference with a coverageData >= 1X There is a 1.45% of reference with a coverageData >= 2X There is a 1.12% of reference with a coverageData >= 3X There is a 0.92% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.57% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 25578611 0.10262205525257247 1.3466636907768412 chr2 243199373 24102603 0.09910635337040939 3.7989570282144607 chr3 198022430 22363930 0.11293634766526196 0.9807152664082606 chr4 191154276 16773777 0.08774994392487459 0.9327034141912686 chr5 180915260 18496558 0.10223879400775811 0.9321820282303562 chr6 171115067 15257650 0.08916602300135265 0.8813984897200969 chr7 159138663 20497246 0.1288011700839789 1.241000403528876 chr8 146364022 10893974 0.07443068215220268 0.8554731169692145 chr9 141213431 11214538 0.07941551961866856 0.8925549645591928 chr10 135534747 11419607 0.08425593622866319 1.4111410780321467 chr11 135006516 13562395 0.1004573364444128 0.9272107005384405 chr12 133851895 9836711 0.07348951615515044 0.7877606511422668 chr13 115169878 9061953 0.0786833602445945 0.8189012795995914 chr14 107349540 6664618 0.06208334008697196 0.7271131861725841 chr15 102531392 6059745 0.05910136282944447 0.6914324910631571 chr16 90354753 11047537 0.12226846550064721 1.253301857960621 chr17 81195210 6476458 0.07976404026789265 0.8464930382199006 chr18 78077248 4459837 0.05712082731194624 1.0361060580952695 chr19 59128983 4870942 0.0823782475676945 1.2194796933136915 chr20 63025520 8365144 0.13272629880721334 1.039714693904121 chr21 48129895 3076294 0.06391649098756605 0.7495742588337283 chr22 51304566 2499124 0.04871153183519767 0.6059472027045538 chrMT 16571 664851 40.12135658680828 33.76066079730033 chrX 155270560 8971334 0.057778718644410115 0.6890387415059885 chrY 59373566 408623 0.0068822377958568295 0.3195250993070428