BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008746.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,994,429 number of mapped reads = 1,496,232 (75.02%) number of supplementary alignments = 12,161 (0.61%) number of secondary alignments = 0 number of mapped bases = 92,581,910 bp number of sequenced bases = 92,533,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,653 duplication rate = 7.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.679 >>>>>>> ACTG content number of A's = 24,788,764 bp (26.79%) number of C's = 16,032,862 bp (17.33%) number of T's = 30,301,736 bp (32.75%) number of G's = 21,386,217 bp (23.11%) number of N's = 24,410 bp (0.03%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 780,139 number of insertions = 7,455 mapped reads with insertion percentage = 0.49% number of deletions = 29,050 mapped reads with deletion percentage = 1.92% homopolymer indels = 46.06% >>>>>>> Coverage mean coverageData = 0.0299X std coverageData = 0.3354X There is a 2.2% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 16784138 0.0673383999312082 0.6965172658223141 chr2 243199373 8672610 0.035660494897739724 0.31930222246587425 chr3 198022430 12434682 0.06279431072530521 0.3424559960115295 chr4 191154276 4598063 0.024054199028223675 0.2011459853257636 chr5 180915260 3504076 0.019368603842484046 0.17932692048809548 chr6 171115067 2371370 0.013858335455638164 0.18088690903795568 chr7 159138663 3468632 0.021796287178810846 0.22772798974214511 chr8 146364022 2207355 0.01508126771755425 0.17336993106800086 chr9 141213431 3205321 0.022698414572194625 0.22427635565510054 chr10 135534747 6146844 0.04535253236574087 0.6574516141396658 chr11 135006516 2066395 0.015305890865297198 0.28304503403577463 chr12 133851895 1919809 0.014342785359893485 0.15736539165366323 chr13 115169878 1270603 0.011032424641450085 0.13568986764345214 chr14 107349540 4208656 0.03920516100953949 0.25773807508319957 chr15 102531392 1568519 0.015297939191150356 0.1604636518207601 chr16 90354753 1390980 0.015394652232627983 0.2589136444317302 chr17 81195210 1178560 0.014515141964655304 0.19030982010893116 chr18 78077248 928792 0.011895808622762934 0.3926071928942058 chr19 59128983 3214189 0.054358942720188506 0.43860621826925317 chr20 63025520 1493350 0.023694370153550498 0.19792424423561175 chr21 48129895 530642 0.011025205851789205 0.14109589573357054 chr22 51304566 980496 0.019111281440330283 0.17565278268750886 chrMT 16571 46524 2.8075553678112364 2.615503861365667 chrX 155270560 8107506 0.052215345909746184 0.32111411535902035 chrY 59373566 283798 0.004779871230911076 0.1296350800753831