BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173848.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 = 13,055,734 number of mapped reads = 12,693,166 (97.22%) number of supplementary alignments = 1,286,718 (9.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,365,623 number of mapped paired reads (second in pair) = 6,327,543 number of mapped paired reads (both in pair) = 12,449,390 number of mapped paired reads (singletons) = 243,776 number of mapped bases = 1,501,299,945 bp number of sequenced bases = 1,500,432,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,949,359 duplication rate = 64.69% >>>>>>> Insert size mean insert size = 867,430.8462 std insert size = 8,490,993.3038 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 52.6458 >>>>>>> ACTG content number of A's = 450,696,018 bp (30.04%) number of C's = 294,883,509 bp (19.65%) number of T's = 449,486,344 bp (29.96%) number of G's = 305,349,244 bp (20.35%) number of N's = 17,105 bp (0%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 15,822,243 number of insertions = 161,365 mapped reads with insertion percentage = 1.23% number of deletions = 354,542 mapped reads with deletion percentage = 2.73% homopolymer indels = 42.8% >>>>>>> Coverage mean coverageData = 0.485X std coverageData = 6.6742X There is a 9.4% of reference with a coverageData >= 1X There is a 7.55% of reference with a coverageData >= 2X There is a 5.96% of reference with a coverageData >= 3X There is a 4.97% of reference with a coverageData >= 4X There is a 3.87% of reference with a coverageData >= 5X There is a 3.16% of reference with a coverageData >= 6X There is a 2.41% of reference with a coverageData >= 7X There is a 1.96% of reference with a coverageData >= 8X There is a 1.49% of reference with a coverageData >= 9X There is a 1.23% of reference with a coverageData >= 10X There is a 0.94% of reference with a coverageData >= 11X There is a 0.8% of reference with a coverageData >= 12X There is a 0.61% of reference with a coverageData >= 13X There is a 0.52% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 134738751 0.5405753873728564 3.4673450470961007 chr2 243199373 112692104 0.46337333279226833 20.347252620436038 chr3 198022430 92735319 0.46830714581171434 2.0080783944325025 chr4 191154276 91628125 0.4793412259320843 3.3614668601671474 chr5 180915260 75617672 0.4179728785730955 1.861664284895835 chr6 171115067 73475336 0.4293913872587269 2.1084886935951728 chr7 159138663 132500448 0.8326100364435008 7.103867329616007 chr8 146364022 145318147 0.9928542890137304 4.096706379881613 chr9 141213431 52339860 0.3706436394141574 2.8055665428777945 chr10 135534747 69941485 0.5160409898429957 8.405702029875377 chr11 135006516 61879077 0.4583414107212425 2.1740896798651517 chr12 133851895 57398211 0.4288188150044495 1.9151052058116567 chr13 115169878 38585120 0.33502787942520873 1.681534612060983 chr14 107349540 50508869 0.47050848098650444 2.029221098847765 chr15 102531392 36385747 0.35487421257286744 1.7250715333785354 chr16 90354753 35749432 0.39565635246659353 3.2043540024108044 chr17 81195210 41127394 0.5065248799775258 2.5531165812100967 chr18 78077248 26878459 0.3442546924809645 4.31275543225051 chr19 59128983 17538136 0.29660811179519186 2.6878398835335404 chr20 63025520 57990735 0.9201151374871639 2.9438413763279905 chr21 48129895 18233716 0.3788438765553093 2.143258632138457 chr22 51304566 14712382 0.2867655483139649 1.516402441805549 chrMT 16571 3976129 239.94502444028726 164.27928864923268 chrX 155270560 56311796 0.36266885364488927 1.793605734197304 chrY 59373566 3037495 0.0511590460980565 2.144147904151713