BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174042.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 = 4,134,702 number of mapped reads = 4,037,406 (97.65%) number of supplementary alignments = 419,627 (10.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,018,669 number of mapped paired reads (second in pair) = 2,018,737 number of mapped paired reads (both in pair) = 3,971,978 number of mapped paired reads (singletons) = 65,428 number of mapped bases = 479,427,991 bp number of sequenced bases = 479,151,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,146,748 duplication rate = 64.64% >>>>>>> Insert size mean insert size = 938,478.5523 std insert size = 8,915,841.9372 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.7327 >>>>>>> ACTG content number of A's = 145,337,370 bp (30.33%) number of C's = 92,749,392 bp (19.36%) number of T's = 145,024,877 bp (30.27%) number of G's = 96,033,878 bp (20.04%) number of N's = 6,222 bp (0%) GC percentage = 39.4% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 4,751,660 number of insertions = 48,972 mapped reads with insertion percentage = 1.17% number of deletions = 109,872 mapped reads with deletion percentage = 2.66% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.1549X std coverageData = 2.3295X There is a 3.25% of reference with a coverageData >= 1X There is a 2.53% of reference with a coverageData >= 2X There is a 1.94% of reference with a coverageData >= 3X There is a 1.59% of reference with a coverageData >= 4X There is a 1.21% of reference with a coverageData >= 5X There is a 0.99% of reference with a coverageData >= 6X There is a 0.74% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.18% 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 0.1% 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 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.02% 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 45192070 0.18131176491632492 1.436291612851599 chr2 243199373 35141287 0.14449579604796103 6.514332210248414 chr3 198022430 30103458 0.1520204453606594 1.1464487922399127 chr4 191154276 29603602 0.15486758977863513 1.3427018155063493 chr5 180915260 24243893 0.13400689914162023 1.062509617278356 chr6 171115067 24003414 0.14027644918024665 1.122700414383009 chr7 159138663 38709832 0.24324592949483306 2.403172537063187 chr8 146364022 47282418 0.3230467252396221 1.9441221097863557 chr9 141213431 16386198 0.11603852327616061 1.1571024990865018 chr10 135534747 22041928 0.1626293514238087 3.364827609034986 chr11 135006516 19142834 0.1417919265467157 1.1059043218889648 chr12 133851895 18570846 0.1387417488560771 1.0839062363649044 chr13 115169878 12783685 0.11099851126003624 0.976529991982699 chr14 107349540 16779989 0.15631169914654502 1.14911045374941 chr15 102531392 11530972 0.11246284455008668 0.9649196810104265 chr16 90354753 10871916 0.12032478247159836 1.2625040603221909 chr17 81195210 11666311 0.14368225662572953 1.2108215575232109 chr18 78077248 8659465 0.11090894238485455 1.5225430469543242 chr19 59128983 7120264 0.1204191859684108 1.1529594561286298 chr20 63025520 18208430 0.2889056686878585 1.5623321452980987 chr21 48129895 5958274 0.12379569911798062 1.0577305906591044 chr22 51304566 5429798 0.10583459569660915 0.893707171255319 chrMT 16571 1045507 63.09257135960413 56.96012117069748 chrX 155270560 18157927 0.11694378509358117 0.9970933863253153 chrY 59373566 793673 0.0133674470554792 0.5833015411354464