BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716625.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 = 876,056 number of mapped reads = 653,625 (74.61%) number of supplementary alignments = 2,939 (0.34%) number of secondary alignments = 0 number of mapped bases = 37,664,732 bp number of sequenced bases = 37,653,389 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,664 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8599 >>>>>>> ACTG content number of A's = 9,984,888 bp (26.52%) number of C's = 6,756,768 bp (17.94%) number of T's = 11,707,325 bp (31.09%) number of G's = 9,203,299 bp (24.44%) number of N's = 1,109 bp (0%) GC percentage = 42.39% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 193,762 number of insertions = 2,601 mapped reads with insertion percentage = 0.4% number of deletions = 7,040 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.25% >>>>>>> Coverage mean coverageData = 0.0122X std coverageData = 0.1424X There is a 1.14% of reference with a coverageData >= 1X There is a 0.05% 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 3045291 0.012217787012053222 0.2254448553492193 chr2 243199373 3198347 0.013151131767103693 0.17706612759409132 chr3 198022430 2487794 0.01256319296758453 0.11807125032758202 chr4 191154276 2421060 0.012665476549423358 0.12244738521727662 chr5 180915260 2251730 0.012446324317804921 0.11666918561973609 chr6 171115067 2177225 0.012723748049609214 0.12758993836917823 chr7 159138663 2088469 0.013123580157261972 0.16362423769296996 chr8 146364022 1905760 0.013020686190216882 0.13810916916362648 chr9 141213431 1527421 0.0108164003181822 0.1271156044482997 chr10 135534747 1801167 0.013289337530544842 0.14047965183080663 chr11 135006516 1719879 0.012739229564297475 0.1296174481294739 chr12 133851895 1696949 0.012677810799764919 0.1190495473516013 chr13 115169878 1165721 0.010121752495040413 0.10498819676820033 chr14 107349540 1145700 0.010672612104346233 0.11124970211466575 chr15 102531392 1104053 0.01076795095106092 0.10940884423342352 chr16 90354753 1104469 0.01222369563668665 0.1201923046048984 chr17 81195210 1035527 0.012753547900177855 0.12022759688956 chr18 78077248 1015334 0.013004223714442395 0.18679720873418795 chr19 59128983 789718 0.01335585291565052 0.16765855170195504 chr20 63025520 787076 0.012488211124636496 0.1176460228702439 chr21 48129895 506948 0.010532913067855228 0.11139281296108067 chr22 51304566 465660 0.009076385131101197 0.10015079339160143 chrMT 16571 2747 0.16577152857401484 0.44083193175367497 chrX 155270560 2106956 0.013569578160856766 0.12671603748615445 chrY 59373566 113731 0.0019155157364137434 0.06262981826399305