BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008676.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 = 1,675,468 number of mapped reads = 1,492,342 (89.07%) number of supplementary alignments = 8,024 (0.48%) number of secondary alignments = 0 number of mapped bases = 97,092,185 bp number of sequenced bases = 97,021,716 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,342 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4291 >>>>>>> ACTG content number of A's = 26,938,639 bp (27.77%) number of C's = 17,571,724 bp (18.11%) number of T's = 30,692,913 bp (31.64%) number of G's = 21,780,740 bp (22.45%) number of N's = 37,700 bp (0.04%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 851,124 number of insertions = 7,047 mapped reads with insertion percentage = 0.47% number of deletions = 39,957 mapped reads with deletion percentage = 2.63% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.3781X There is a 2.76% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8954295 0.03592486535871058 0.8538516765785423 chr2 243199373 9663392 0.039734444545628 0.39738452453101214 chr3 198022430 6808401 0.03438196874970174 0.22865547017617988 chr4 191154276 5004263 0.026179184189424044 0.1932279002807412 chr5 180915260 4361674 0.02410893365214189 0.17242500539092362 chr6 171115067 5227960 0.03055230665339365 0.21423314427564696 chr7 159138663 6189499 0.03889374764949483 0.3963714309995761 chr8 146364022 5484309 0.03747033543530254 0.41635812303437264 chr9 141213431 3582741 0.02537110652031392 0.2944421127195263 chr10 135534747 5388174 0.03975492719959111 0.5704123209104447 chr11 135006516 3403935 0.02521311638024938 0.23841045715233675 chr12 133851895 4405027 0.0329097096458739 0.2000639991382663 chr13 115169878 2139503 0.018576932068991164 0.14785779305800484 chr14 107349540 4313671 0.040183413920544045 0.22833628078022128 chr15 102531392 2798740 0.027296420592826828 0.18014409594077072 chr16 90354753 2247042 0.024869106775157693 0.20866203420598353 chr17 81195210 2598563 0.032003895303676165 0.2395924601563273 chr18 78077248 1691747 0.02166760539510819 0.5079067529443266 chr19 59128983 2246839 0.0379989454579322 0.48880834646349786 chr20 63025520 2208117 0.035035284119829556 0.2084451661856624 chr21 48129895 1202252 0.02497931898667138 0.18881722386364785 chr22 51304566 1188474 0.023165072675987552 0.16405523539096734 chrMT 16571 153542 9.26570514754692 5.250000640568294 chrX 155270560 5527806 0.03560112103672454 0.22962123571322463 chrY 59373566 302219 0.005090127145133913 0.16524975662192562