BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173880.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 = 5,298,102 number of mapped reads = 5,161,542 (97.42%) number of supplementary alignments = 533,780 (10.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,581,188 number of mapped paired reads (second in pair) = 2,580,354 number of mapped paired reads (both in pair) = 5,068,522 number of mapped paired reads (singletons) = 93,020 number of mapped bases = 610,555,321 bp number of sequenced bases = 610,202,318 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,065,401 duplication rate = 65.16% >>>>>>> Insert size mean insert size = 951,286.6777 std insert size = 8,766,194.9849 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.6712 >>>>>>> ACTG content number of A's = 184,287,087 bp (30.2%) number of C's = 118,828,376 bp (19.47%) number of T's = 183,975,478 bp (30.15%) number of G's = 123,104,473 bp (20.17%) number of N's = 6,904 bp (0%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 6,091,573 number of insertions = 62,647 mapped reads with insertion percentage = 1.18% number of deletions = 142,006 mapped reads with deletion percentage = 2.68% homopolymer indels = 42.64% >>>>>>> Coverage mean coverageData = 0.1972X std coverageData = 2.9949X There is a 4% of reference with a coverageData >= 1X There is a 3.15% of reference with a coverageData >= 2X There is a 2.44% of reference with a coverageData >= 3X There is a 2.02% of reference with a coverageData >= 4X There is a 1.56% of reference with a coverageData >= 5X There is a 1.28% of reference with a coverageData >= 6X There is a 0.96% of reference with a coverageData >= 7X There is a 0.79% of reference with a coverageData >= 8X There is a 0.59% of reference with a coverageData >= 9X There is a 0.5% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 55472742 0.22255808943400787 1.7601976406958928 chr2 243199373 45484689 0.1870263415522868 8.776310910494924 chr3 198022430 39837949 0.2011789725032664 1.3399813703342398 chr4 191154276 39404460 0.20613956864872854 1.6141997534670178 chr5 180915260 29404658 0.1625327681036967 1.183051563409153 chr6 171115067 27786843 0.16238688671407295 1.2312639663218807 chr7 159138663 54552337 0.34279750735369696 3.2830058907889956 chr8 146364022 62053416 0.42396632145022634 2.2932063702412995 chr9 141213431 21041699 0.1490063576176405 1.4221846545845707 chr10 135534747 23184205 0.17105727876556998 3.66513320347001 chr11 135006516 25605359 0.1896601716616404 1.3002435540718136 chr12 133851895 22901535 0.171096083473454 1.218702300894935 chr13 115169878 16015487 0.1390596853805819 1.09682489476565 chr14 107349540 20353056 0.18959611750548722 1.2868880815467991 chr15 102531392 14459704 0.14102709148823417 1.0822774202624343 chr16 90354753 14005285 0.1550033012651808 1.469712102283768 chr17 81195210 14943902 0.18404905905163618 1.3344090416806456 chr18 78077248 11123694 0.14247036473416685 1.756334055677472 chr19 59128983 9287901 0.15707865295095638 1.4187761535491235 chr20 63025520 23459714 0.3722256317758267 1.820226264183486 chr21 48129895 8075353 0.16778247698234122 1.2780836458469653 chr22 51304566 6615454 0.12894474148753154 1.007638802473802 chrMT 16571 1106999 66.8033914670207 60.93332976653418 chrX 155270560 23264889 0.14983451466910405 1.1522853237304969 chrY 59373566 1113991 0.018762406825960226 0.8525254227705479