BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717066.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 824,676 number of mapped reads = 709,428 (86.03%) number of supplementary alignments = 3,138 (0.38%) number of secondary alignments = 0 number of mapped bases = 40,062,207 bp number of sequenced bases = 40,050,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,708 duplication rate = 1.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9141 >>>>>>> ACTG content number of A's = 9,693,154 bp (24.2%) number of C's = 8,440,829 bp (21.08%) number of T's = 11,284,650 bp (28.18%) number of G's = 10,630,646 bp (26.54%) number of N's = 1,132 bp (0%) GC percentage = 47.62% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 211,678 number of insertions = 3,619 mapped reads with insertion percentage = 0.51% number of deletions = 6,787 mapped reads with deletion percentage = 0.95% homopolymer indels = 33.53% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 0.1365X There is a 1.2% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% 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 3885779 0.01558984681526631 0.15509779048585606 chr2 243199373 3445251 0.014166364647658858 0.15927227829392124 chr3 198022430 2660215 0.01343390746189712 0.12550056035087365 chr4 191154276 2600991 0.013606763366360687 0.14501317456954047 chr5 180915260 2398813 0.01325931820234512 0.12136522021270589 chr6 171115067 1677697 0.00980449605878365 0.10623787630603748 chr7 159138663 2327585 0.014626143993681787 0.14679781251867682 chr8 146364022 2475163 0.0169110069959679 0.14319117803963347 chr9 141213431 1758372 0.012451875062790593 0.12356200608513614 chr10 135534747 2135287 0.015754535624728026 0.21049745247030097 chr11 135006516 1637316 0.01212768130391573 0.12971610263581876 chr12 133851895 1895060 0.014157886969026475 0.12630311322765228 chr13 115169878 695837 0.006041831528205665 0.08327597100720269 chr14 107349540 1246176 0.011608582579860147 0.11632019888575258 chr15 102531392 817301 0.007971226997483854 0.09565134099013367 chr16 90354753 1103443 0.012212340395640283 0.12633496489638688 chr17 81195210 1605001 0.019767188236843036 0.1557294850608397 chr18 78077248 1097732 0.014059563164931224 0.14776878671411994 chr19 59128983 1090126 0.018436407066226727 0.16020621365537197 chr20 63025520 1069490 0.016969157890327602 0.1465083657404245 chr21 48129895 545941 0.011343074818675586 0.12688217925142112 chr22 51304566 463435 0.009033016671459613 0.10257603822005823 chrMT 16571 49597 2.9929998189608353 2.9556693882040377 chrX 155270560 1241572 0.007996184209034862 0.09858721725164361 chrY 59373566 139027 0.0023415639208869484 0.08997087773194329