BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524689.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 = 2,043,369 number of mapped reads = 1,862,990 (91.17%) number of supplementary alignments = 7,353 (0.36%) number of secondary alignments = 0 number of mapped bases = 106,574,430 bp number of sequenced bases = 106,538,699 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,833 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.868 >>>>>>> ACTG content number of A's = 27,135,399 bp (25.47%) number of C's = 18,991,671 bp (17.83%) number of T's = 35,281,227 bp (33.12%) number of G's = 25,128,389 bp (23.59%) number of N's = 2,013 bp (0%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 543,845 number of insertions = 8,024 mapped reads with insertion percentage = 0.43% number of deletions = 22,443 mapped reads with deletion percentage = 1.2% homopolymer indels = 42.91% >>>>>>> Coverage mean coverageData = 0.0344X std coverageData = 0.3324X There is a 3.08% of reference with a coverageData >= 1X There is a 0.26% 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 11469199 0.046014725877052076 0.6249051898677325 chr2 243199373 9234591 0.03797127799338529 0.4579626610942875 chr3 198022430 8658347 0.04372407206597757 0.2304624360860972 chr4 191154276 6256819 0.03273177629570787 0.20902286060253294 chr5 180915260 4945386 0.027335372372678787 0.18180253505348526 chr6 171115067 5476871 0.03200694769911758 0.2342629731697674 chr7 159138663 6856937 0.04308781329902212 0.5062096358431497 chr8 146364022 5027158 0.03434695173927374 0.32141464585850427 chr9 141213431 3468600 0.024562819382244173 0.22838845157970056 chr10 135534747 5800701 0.04279862639209413 0.34828762262226554 chr11 135006516 4957708 0.03672199051488744 0.27099403686861107 chr12 133851895 4832894 0.03610628000447808 0.21177365282892102 chr13 115169878 3465057 0.030086486676663842 0.19355722926274563 chr14 107349540 4006048 0.037317793816349844 0.21835765139069097 chr15 102531392 2942536 0.028698878876042177 0.19193538925931664 chr16 90354753 2837260 0.031401336463174216 0.21733005664983432 chr17 81195210 2093714 0.025786176302764658 0.18313881863322698 chr18 78077248 2322814 0.029750203285853517 0.46173502663573035 chr19 59128983 1846159 0.03122257320069246 0.4316210333431206 chr20 63025520 1942028 0.030813359413773975 0.19594189609357304 chr21 48129895 1398419 0.029055101823928765 0.19812804938138331 chr22 51304566 813126 0.015848998703156363 0.1371687106593598 chrMT 16571 100025 6.036147486572928 3.851414883941298 chrX 155270560 5512750 0.035504154812090585 0.23218194355993313 chrY 59373566 309283 0.005209102650159164 0.14580897407542887