BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173905.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 = 4,471,152 number of mapped reads = 4,355,926 (97.42%) number of supplementary alignments = 442,386 (9.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,182,890 number of mapped paired reads (second in pair) = 2,173,036 number of mapped paired reads (both in pair) = 4,281,412 number of mapped paired reads (singletons) = 74,514 number of mapped bases = 517,245,016 bp number of sequenced bases = 516,920,869 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,369,044 duplication rate = 64.26% >>>>>>> Insert size mean insert size = 1,375,805.3907 std insert size = 11,023,510.1462 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 52.952 >>>>>>> ACTG content number of A's = 154,493,976 bp (29.89%) number of C's = 101,979,521 bp (19.73%) number of T's = 154,268,273 bp (29.84%) number of G's = 106,173,069 bp (20.54%) number of N's = 6,030 bp (0%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 5,545,282 number of insertions = 58,652 mapped reads with insertion percentage = 1.3% number of deletions = 135,505 mapped reads with deletion percentage = 3.03% homopolymer indels = 42.34% >>>>>>> Coverage mean coverageData = 0.1671X std coverageData = 2.3399X There is a 3.6% of reference with a coverageData >= 1X There is a 2.82% of reference with a coverageData >= 2X There is a 2.17% of reference with a coverageData >= 3X There is a 1.77% of reference with a coverageData >= 4X There is a 1.34% of reference with a coverageData >= 5X There is a 1.07% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.63% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.27% 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 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% 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% 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 40451294 0.16229164781097977 1.5703479217185694 chr2 243199373 44497970 0.18296909836194356 6.792784624087148 chr3 198022430 35769656 0.1806343655110181 1.2117907936029695 chr4 191154276 36263812 0.18970965629876885 1.6184009979070209 chr5 180915260 35171934 0.19441109611206928 1.2584804767118656 chr6 171115067 29211533 0.17071280461819296 1.36025401096187 chr7 159138663 26620274 0.16727722539682263 1.347162437886041 chr8 146364022 26965963 0.18423901332801582 1.6934134723955288 chr9 141213431 22750635 0.16110815266573333 1.498057363384682 chr10 135534747 24387121 0.17993261167189842 2.034530556294638 chr11 135006516 22424903 0.16610237538460737 1.1694732759699369 chr12 133851895 24538743 0.18332757261299887 1.22244179267368 chr13 115169878 18802432 0.1632582436181794 1.153589742181228 chr14 107349540 16581913 0.15446654918130065 1.1164972334239087 chr15 102531392 16832741 0.16417158366483506 1.131966787261812 chr16 90354753 15911025 0.1760950527970565 1.4731677136798564 chr17 81195210 15375739 0.1893675624461098 1.3307107315714921 chr18 78077248 14288592 0.1830058354515774 2.1061886195680555 chr19 59128983 9672874 0.16358938559792244 1.3912653345532897 chr20 63025520 11444732 0.18158885480040465 1.2500200231138199 chr21 48129895 4943426 0.10271009317597722 1.390099348154732 chr22 51304566 6572602 0.12810949419199844 1.1062235608643107 chrMT 16571 872723 52.66568100899161 43.01524418849007 chrX 155270560 12214469 0.07866571100149314 0.7884202407491377 chrY 59373566 4677910 0.07878775548027551 1.2855459279790016