BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524948.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 = 1,780,021 number of mapped reads = 1,643,377 (92.32%) number of supplementary alignments = 4,611 (0.26%) number of secondary alignments = 0 number of mapped bases = 97,150,171 bp number of sequenced bases = 97,117,638 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,389 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7274 >>>>>>> ACTG content number of A's = 25,550,538 bp (26.31%) number of C's = 16,596,764 bp (17.09%) number of T's = 30,589,214 bp (31.5%) number of G's = 24,379,984 bp (25.1%) number of N's = 1,138 bp (0%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 466,430 number of insertions = 6,742 mapped reads with insertion percentage = 0.41% number of deletions = 19,069 mapped reads with deletion percentage = 1.15% homopolymer indels = 43.54% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.2875X There is a 2.83% 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 0.01% 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 10171516 0.040808387795350766 0.5561972173765022 chr2 243199373 9232260 0.03796169326472729 0.3151590554317732 chr3 198022430 5284897 0.02668837565522249 0.17696525269856456 chr4 191154276 6161849 0.032234952463213534 0.20974931167154617 chr5 180915260 4186966 0.02314324396958001 0.16677937229075754 chr6 171115067 6520237 0.03810440023963524 0.29292779037842176 chr7 159138663 6025029 0.037860246444322586 0.3923842626773093 chr8 146364022 6334100 0.04327634560356643 0.3030719052242653 chr9 141213431 2647153 0.0187457593888502 0.21546543040457644 chr10 135534747 4881432 0.036016092611291774 0.2784951131103535 chr11 135006516 4024052 0.02980635393924246 0.257121695184351 chr12 133851895 5206044 0.03889406272507386 0.21378642299651357 chr13 115169878 2708891 0.023520828944526624 0.16662680416656528 chr14 107349540 2168458 0.020199974773995304 0.1602475870126057 chr15 102531392 2624269 0.025594785643795803 0.18889609246008043 chr16 90354753 2990580 0.03309820347801737 0.20521614637057395 chr17 81195210 2605962 0.03209502136887139 0.2714698483174423 chr18 78077248 1902510 0.02436702174748782 0.36927689086761667 chr19 59128983 2241633 0.037910900649179104 0.33877088218312107 chr20 63025520 2272790 0.03606142400729102 0.20728827791233234 chr21 48129895 1374067 0.02854913770329231 0.19382693540528162 chr22 51304566 1221316 0.023805210631739872 0.16495375844460622 chrMT 16571 8743 0.5276084726329129 0.783492595107183 chrX 155270560 4101011 0.026412032004006426 0.20631967975019053 chrY 59373566 254406 0.004284836117136707 0.10189411859429738