BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174071.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 = 3,785,026 number of mapped reads = 3,699,411 (97.74%) number of supplementary alignments = 519,211 (13.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,850,897 number of mapped paired reads (second in pair) = 1,848,514 number of mapped paired reads (both in pair) = 3,642,178 number of mapped paired reads (singletons) = 57,233 number of mapped bases = 421,389,884 bp number of sequenced bases = 421,055,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,979,521 duplication rate = 64.94% >>>>>>> Insert size mean insert size = 1,241,854.0948 std insert size = 10,587,126.073 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.514 >>>>>>> ACTG content number of A's = 125,055,083 bp (29.7%) number of C's = 84,062,478 bp (19.96%) number of T's = 124,111,486 bp (29.48%) number of G's = 87,823,021 bp (20.86%) number of N's = 3,329 bp (0%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,644,953 number of insertions = 47,332 mapped reads with insertion percentage = 1.23% number of deletions = 145,023 mapped reads with deletion percentage = 3.82% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 0.1361X std coverageData = 2.704X There is a 2.97% of reference with a coverageData >= 1X There is a 2.23% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 1.33% of reference with a coverageData >= 4X There is a 0.99% of reference with a coverageData >= 5X There is a 0.81% of reference with a coverageData >= 6X There is a 0.6% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 33485472 0.13434458805219987 1.3401819042164358 chr2 243199373 34683358 0.14261285945009405 8.648407401160148 chr3 198022430 27218382 0.1374510049189882 1.1023245248733564 chr4 191154276 28967768 0.1515413026910264 1.4345756329422972 chr5 180915260 27964193 0.1545706702685003 1.1757281647546598 chr6 171115067 25543537 0.14927695993012702 1.247821905618763 chr7 159138663 22210141 0.13956470779197133 1.219757420369949 chr8 146364022 20257914 0.13840774340021894 1.4155311633588286 chr9 141213431 18260838 0.12931374778366514 1.2253883916682722 chr10 135534747 21330129 0.15737756901556765 1.6846008236528551 chr11 135006516 20529352 0.1520619345513664 1.1836314174949167 chr12 133851895 20933045 0.15638960509300223 1.1892038737903732 chr13 115169878 14028629 0.12180814327162871 1.0531675567210974 chr14 107349540 12413653 0.11563769160072787 1.0125510879694042 chr15 102531392 12156815 0.11856676050979587 1.0281054479466183 chr16 90354753 13421682 0.14854428299970007 1.2706966645579991 chr17 81195210 12533530 0.1543629236256671 1.230686683488276 chr18 78077248 11715246 0.15004686128281572 1.6535799238725315 chr19 59128983 9067212 0.15334632087279432 1.254307779154973 chr20 63025520 9517787 0.15101481114316867 1.1909247064975383 chr21 48129895 5793285 0.12036770493681734 1.1500990587436266 chr22 51304566 5145302 0.10028935826101716 1.0240970459714354 chrMT 16571 762723 46.02757829943878 38.45234307009213 chrX 155270560 10150946 0.06537585747098484 0.7510965697498873 chrY 59373566 3298945 0.055562520869977726 1.0368861327580892