BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716172.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 = 552,945 number of mapped reads = 514,205 (92.99%) number of supplementary alignments = 10,743 (1.94%) number of secondary alignments = 0 number of mapped bases = 40,491,123 bp number of sequenced bases = 40,473,318 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,146 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3141 >>>>>>> ACTG content number of A's = 10,387,297 bp (25.66%) number of C's = 7,700,683 bp (19.03%) number of T's = 12,199,021 bp (30.14%) number of G's = 10,183,129 bp (25.16%) number of N's = 3,188 bp (0.01%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 257,514 number of insertions = 3,199 mapped reads with insertion percentage = 0.61% number of deletions = 9,164 mapped reads with deletion percentage = 1.75% homopolymer indels = 44.72% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.153X There is a 1.22% of reference with a coverageData >= 1X There is a 0.06% 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 3889986 0.015606725409121449 0.26589791599266527 chr2 243199373 3376999 0.01388572247675984 0.1616217529290708 chr3 198022430 2526363 0.012757963832682994 0.11741187921929387 chr4 191154276 2524808 0.01320822140541601 0.13455719470224725 chr5 180915260 2374920 0.013127250846611834 0.11938138280880023 chr6 171115067 2339347 0.013671192379569942 0.12617083522292732 chr7 159138663 2156917 0.013553695622037494 0.17713468358390383 chr8 146364022 2018953 0.013794052475546211 0.16116982514387534 chr9 141213431 1713297 0.012132677379675025 0.1359379310456353 chr10 135534747 1862948 0.013745168978697396 0.15612281964523766 chr11 135006516 2287642 0.01694467843315059 0.16697190549845878 chr12 133851895 1772587 0.01324289805534692 0.11956404012942348 chr13 115169878 1349588 0.011718237645437116 0.1124452058841602 chr14 107349540 1076082 0.010024095119550581 0.1059510443766452 chr15 102531392 1128447 0.011005868329574614 0.10914735724174107 chr16 90354753 897562 0.009933755228128397 0.10701125972825595 chr17 81195210 1260775 0.015527701695703479 0.13884103357903352 chr18 78077248 1049899 0.013446926305599296 0.1873334526158095 chr19 59128983 807499 0.01365656838711398 0.1944366480268346 chr20 63025520 822573 0.01305142742178089 0.12111415757184549 chr21 48129895 507819 0.01055100992844468 0.11723681487096621 chr22 51304566 454586 0.008860536896462587 0.09764653811807882 chrMT 16571 2897 0.17482348681431417 0.4177497764535928 chrX 155270560 2164273 0.01393872090111609 0.12951735124951552 chrY 59373566 124356 0.0020944674268006743 0.0867236525941034