BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524889.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 = 743,327 number of mapped reads = 661,373 (88.97%) number of supplementary alignments = 3,244 (0.44%) number of secondary alignments = 0 number of mapped bases = 39,767,054 bp number of sequenced bases = 39,753,909 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,532 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9124 >>>>>>> ACTG content number of A's = 10,789,461 bp (27.14%) number of C's = 7,398,760 bp (18.61%) number of T's = 12,566,843 bp (31.61%) number of G's = 8,998,030 bp (22.63%) number of N's = 815 bp (0%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 192,941 number of insertions = 2,904 mapped reads with insertion percentage = 0.44% number of deletions = 8,062 mapped reads with deletion percentage = 1.21% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.0128X std coverageData = 0.1536X There is a 1.21% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4084484 0.016387056463943575 0.25087944586976235 chr2 243199373 2500562 0.010281942626554387 0.14726627972152775 chr3 198022430 2841718 0.014350485447532382 0.12497780981517065 chr4 191154276 2386853 0.012486526851222517 0.11698248788692679 chr5 180915260 1877686 0.0103788149214168 0.10523306821452727 chr6 171115067 2698087 0.01576767637884278 0.13666113017873638 chr7 159138663 3098533 0.019470648688307755 0.2596064563766528 chr8 146364022 2185202 0.014929912215721975 0.15113557899259486 chr9 141213431 1387056 0.00982240846481522 0.11956823269344947 chr10 135534747 1942662 0.014333313360595273 0.1833512704510937 chr11 135006516 1954495 0.014477041982181067 0.13720987477751864 chr12 133851895 1900587 0.014199178876025625 0.12354567305196162 chr13 115169878 985911 0.008560493569334162 0.09563239373786019 chr14 107349540 1921111 0.017895847527618657 0.1397637361025106 chr15 102531392 788662 0.007691907664727696 0.09082091709506447 chr16 90354753 993083 0.010990932596539774 0.11437291814891817 chr17 81195210 699496 0.008614990958210465 0.09779857013715554 chr18 78077248 927804 0.011883154488231962 0.19363890668143136 chr19 59128983 530880 0.008978338085063969 0.17542961296360313 chr20 63025520 712658 0.01130745133082599 0.11009182215186236 chr21 48129895 540424 0.011228447516870752 0.11256681890576678 chr22 51304566 301291 0.005872596212976444 0.07941721473162688 chrMT 16571 87167 5.260213626214471 3.3650502474310517 chrX 155270560 2303606 0.014836077103090244 0.13100290585617055 chrY 59373566 117036 0.0019711802386941017 0.06325650553949586