BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237308.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,386,182 number of mapped reads = 3,329,647 (75.91%) number of supplementary alignments = 16,035 (0.37%) number of secondary alignments = 0 number of mapped bases = 199,660,550 bp number of sequenced bases = 199,542,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,526,440 duplication rate = 22.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.3079 >>>>>>> ACTG content number of A's = 48,821,044 bp (24.47%) number of C's = 34,922,953 bp (17.5%) number of T's = 66,109,359 bp (33.13%) number of G's = 49,669,705 bp (24.89%) number of N's = 19,526 bp (0.01%) GC percentage = 42.39% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,429,408 number of insertions = 14,145 mapped reads with insertion percentage = 0.42% number of deletions = 66,126 mapped reads with deletion percentage = 1.96% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.0645X std coverageData = 1.1224X There is a 1.43% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% 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% 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 22109884 0.08870543195156172 1.2984203220449826 chr2 243199373 20941188 0.08610708054744862 1.679158968250499 chr3 198022430 8841153 0.044647230114285535 0.7827801475482828 chr4 191154276 8620646 0.045097845470116506 0.8203010875131084 chr5 180915260 9506946 0.052549165835983104 0.8764421198388914 chr6 171115067 17781212 0.10391377166103088 1.3075192917172085 chr7 159138663 13974102 0.08781085461299873 1.4599734923735204 chr8 146364022 9330005 0.06374520782163257 1.0167693448222352 chr9 141213431 8558012 0.06060338552357672 1.030663535201354 chr10 135534747 11005723 0.08120222484349346 1.2516595477363592 chr11 135006516 6446076 0.047746406551221574 0.916416452238081 chr12 133851895 7978389 0.059606096723546574 1.001581959934192 chr13 115169878 8739472 0.07588331386441166 1.1102180609102044 chr14 107349540 5095258 0.04746418102956007 0.8344751568325336 chr15 102531392 3559159 0.03471287115657223 0.6842416323627892 chr16 90354753 3448743 0.03816891624948607 0.7190640580591602 chr17 81195210 4020890 0.049521271020790514 0.8579294218495892 chr18 78077248 4868905 0.06236010008959332 1.6997670148475337 chr19 59128983 2735181 0.04625787323282729 0.8408672646784381 chr20 63025520 3462310 0.054935048532721346 0.9397405614389768 chr21 48129895 2637626 0.05480223881643623 0.9277159467451387 chr22 51304566 2459427 0.0479377800408642 0.8816507235311092 chrMT 16571 40095 2.4195884376320076 5.550865894385303 chrX 155270560 12864367 0.08285129518435433 1.2084046098871695 chrY 59373566 635781 0.010708149145025245 0.3541220010552788