BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156416.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 = 2,346,286 number of mapped reads = 2,300,030 (98.03%) number of supplementary alignments = 295,797 (12.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,149,466 number of mapped paired reads (second in pair) = 1,150,564 number of mapped paired reads (both in pair) = 2,271,402 number of mapped paired reads (singletons) = 28,628 number of mapped bases = 261,318,960 bp number of sequenced bases = 261,156,524 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,808,379 duplication rate = 63.64% >>>>>>> Insert size mean insert size = 1,124,496.8106 std insert size = 9,939,012.3858 median insert size = 152 >>>>>>> Mapping quality mean mapping quality = 52.6607 >>>>>>> ACTG content number of A's = 78,246,987 bp (29.96%) number of C's = 51,711,920 bp (19.8%) number of T's = 77,500,174 bp (29.68%) number of G's = 53,695,482 bp (20.56%) number of N's = 1,961 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 2,135,722 number of insertions = 28,176 mapped reads with insertion percentage = 1.18% number of deletions = 68,463 mapped reads with deletion percentage = 2.91% homopolymer indels = 41.81% >>>>>>> Coverage mean coverageData = 0.0844X std coverageData = 1.7465X There is a 1.92% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.6% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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% 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 20370108 0.08172540520972263 0.9801365709833526 chr2 243199373 22732354 0.09347209131168278 5.3617250186770296 chr3 198022430 17612659 0.08894274754632595 0.8835890659005496 chr4 191154276 19754873 0.10334517968094002 1.058947877948133 chr5 180915260 15800042 0.0873339374467361 0.8771217115908297 chr6 171115067 16737678 0.09781533732502937 1.000982460354958 chr7 159138663 14997576 0.094242189278667 0.995535139858061 chr8 146364022 14435683 0.09862863019711224 1.1770971316802066 chr9 141213431 11012305 0.07798341079893456 0.8785106974667998 chr10 135534747 13647006 0.10069009093291774 1.0974026900693556 chr11 135006516 12994157 0.09624836922686013 0.9284398570185343 chr12 133851895 6812675 0.05089711281263519 0.6797197708631577 chr13 115169878 8590012 0.07458557870487628 0.8112839046878567 chr14 107349540 8169856 0.07610517939806728 0.8201397930306054 chr15 102531392 7802009 0.07609385621137378 0.8151846545488287 chr16 90354753 7779490 0.08609939977368983 0.9071015194691538 chr17 81195210 7414711 0.09131956183129522 0.9036279250759792 chr18 78077248 6951089 0.08902835561007479 1.0711407328731577 chr19 59128983 5081330 0.08593636728032343 0.8855636621501023 chr20 63025520 5802616 0.09206772113899259 0.9066177480478935 chr21 48129895 3709927 0.07708155191279766 0.8985023983761676 chr22 51304566 3309616 0.06450919007871542 0.7836706515551785 chrMT 16571 398454 24.045259791201495 21.111218698818014 chrX 155270560 7506703 0.04834595173740598 0.6510358225406749 chrY 59373566 1896031 0.031933924938919785 0.6126581088097339