BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231811.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 = 5,409,381 number of mapped reads = 5,063,063 (93.6%) number of supplementary alignments = 35,714 (0.66%) number of secondary alignments = 0 number of mapped bases = 325,335,855 bp number of sequenced bases = 325,216,412 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 607,937 duplication rate = 9.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0677 >>>>>>> ACTG content number of A's = 84,584,687 bp (26.01%) number of C's = 58,449,691 bp (17.97%) number of T's = 106,229,049 bp (32.66%) number of G's = 75,827,647 bp (23.32%) number of N's = 125,338 bp (0.04%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,992,821 number of insertions = 20,697 mapped reads with insertion percentage = 0.41% number of deletions = 68,019 mapped reads with deletion percentage = 1.33% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.1051X std coverageData = 1.0035X There is a 7.6% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 29152174 0.11695928332310955 1.7804533592290874 chr2 243199373 21968871 0.09033276167204592 1.4953506453525944 chr3 198022430 46439267 0.23451518598170926 0.6447245064438459 chr4 191154276 6867987 0.03592902624893413 0.32900876284907715 chr5 180915260 19606827 0.10837575006110596 0.43905188309399257 chr6 171115067 15777081 0.09220158853691125 0.6411310871369661 chr7 159138663 32302078 0.2029807049466037 2.148647087733045 chr8 146364022 16097254 0.10998094873342576 1.1287100149425155 chr9 141213431 15440881 0.10934428043179548 0.6563891570252138 chr10 135534747 9202083 0.06789464106942258 0.6212970005057747 chr11 135006516 10381281 0.07689466632854965 0.48390824436302077 chr12 133851895 6724014 0.050234731454493045 0.3411193087729431 chr13 115169878 16801278 0.14588257183010994 0.5340400333548913 chr14 107349540 10598108 0.09872522974947075 0.4982165946363905 chr15 102531392 5908779 0.057628974743657045 0.3622840665811054 chr16 90354753 14603407 0.16162300836570268 0.6143160413970981 chr17 81195210 12042400 0.14831416779388834 0.6564862093659586 chr18 78077248 8252347 0.10569464487272912 1.6157509380103572 chr19 59128983 7492437 0.1267134427121806 1.1713266377723432 chr20 63025520 4151861 0.06587587059971897 0.42485548020931707 chr21 48129895 5229698 0.10865799728006886 0.46133556435007905 chr22 51304566 2293003 0.044693936208328906 0.26537047272192515 chrMT 16571 242642 14.642568342284715 8.607582681481164 chrX 155270560 7169897 0.046176796167927775 0.3996563781464712 chrY 59373566 590200 0.009940450603893322 0.2350225659155821