BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524598.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 = 1,674,959 number of mapped reads = 1,560,027 (93.14%) number of supplementary alignments = 3,164 (0.19%) number of secondary alignments = 0 number of mapped bases = 90,701,432 bp number of sequenced bases = 90,672,019 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,819 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2709 >>>>>>> ACTG content number of A's = 23,290,529 bp (25.69%) number of C's = 15,869,228 bp (17.5%) number of T's = 28,524,744 bp (31.46%) number of G's = 22,986,944 bp (25.35%) number of N's = 574 bp (0%) GC percentage = 42.85% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 419,669 number of insertions = 5,678 mapped reads with insertion percentage = 0.36% number of deletions = 17,301 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.33% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.263X There is a 2.59% of reference with a coverageData >= 1X There is a 0.25% 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% 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 8926964 0.03581521267303081 0.45989346540388065 chr2 243199373 8078186 0.03321631096474907 0.29455919073546827 chr3 198022430 6041073 0.03050701377616667 0.19490046883866505 chr4 191154276 4075045 0.021318094919310096 0.1838735248886747 chr5 180915260 5612397 0.03102224212595444 0.1957821959340372 chr6 171115067 5934914 0.03468376048965928 0.2208105415802709 chr7 159138663 5506818 0.03460389760846489 0.34717523728964733 chr8 146364022 8023922 0.0548216828859759 0.3403316608992867 chr9 141213431 2548878 0.018049827002645378 0.22110867036921666 chr10 135534747 3885263 0.028666176652102356 0.25813631760744615 chr11 135006516 5678952 0.042064280808490756 0.28130490509230116 chr12 133851895 3032484 0.02265551787668004 0.17176324157924228 chr13 115169878 2230824 0.01936985641332363 0.15608108570756907 chr14 107349540 1658557 0.015450061546607465 0.14254195576814727 chr15 102531392 2274627 0.022184688568355728 0.1744328647926326 chr16 90354753 2602207 0.028799890582402454 0.19828721490827741 chr17 81195210 1994621 0.024565747166612414 0.17790418508854514 chr18 78077248 2420991 0.03100763746181218 0.3765369619493715 chr19 59128983 1746718 0.02954080911555675 0.32575359629748846 chr20 63025520 1669840 0.026494664383570336 0.18602515344312953 chr21 48129895 813722 0.01690678942889861 0.15942476905873343 chr22 51304566 1602937 0.03124355442359653 0.19702894211701666 chrMT 16571 8375 0.5054010017500452 0.8126050216857486 chrX 155270560 4112386 0.026485291223268596 0.20339543711707808 chrY 59373566 220731 0.003717664524310364 0.1068755436297632