BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234043.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 = 2,707,207 number of mapped reads = 972,085 (35.91%) number of supplementary alignments = 10,035 (0.37%) number of secondary alignments = 0 number of mapped bases = 66,599,792 bp number of sequenced bases = 66,577,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 244,837 duplication rate = 17.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3301 >>>>>>> ACTG content number of A's = 18,682,729 bp (28.06%) number of C's = 12,813,544 bp (19.25%) number of T's = 20,828,911 bp (31.29%) number of G's = 14,224,161 bp (21.36%) number of N's = 28,070 bp (0.04%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 437,612 number of insertions = 4,212 mapped reads with insertion percentage = 0.43% number of deletions = 13,535 mapped reads with deletion percentage = 1.38% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0215X std coverageData = 0.6671X There is a 0.43% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 2331503 0.00935405091728939 0.36428247713517364 chr2 243199373 8143044 0.03348299750756348 0.759433269129461 chr3 198022430 1473078 0.007438945174039123 0.32064960510755425 chr4 191154276 5853015 0.030619325512760174 0.6899095167709554 chr5 180915260 1999628 0.011052843192995439 0.3950452864610245 chr6 171115067 2149537 0.01256193880343687 0.44550381266173217 chr7 159138663 15830327 0.09947505340044235 1.53855742159962 chr8 146364022 1382465 0.009445388156933812 0.4467191647588652 chr9 141213431 884081 0.0062606013729671365 0.29410754364792274 chr10 135534747 5980270 0.044123519114991225 1.0587966873019004 chr11 135006516 1563883 0.011583759409064375 0.38816045932265636 chr12 133851895 5539438 0.04138483059952196 0.8227600142259861 chr13 115169878 1219742 0.01059080743317276 0.5339119620258161 chr14 107349540 1983325 0.01847539356014008 0.5332765451470212 chr15 102531392 847652 0.008267243655484556 0.31330253575471023 chr16 90354753 628704 0.006958172969605705 0.2821493437276486 chr17 81195210 531533 0.006546359077093341 0.23976486402235384 chr18 78077248 2524277 0.03233050683343757 1.5130005994136257 chr19 59128983 846309 0.014312930090476949 0.46696532908334043 chr20 63025520 651641 0.01033931969145197 0.3630654362156146 chr21 48129895 1634267 0.03395534106193251 0.7294179457358339 chr22 51304566 633006 0.012338200073654264 0.42193625181923433 chrMT 16571 18367 1.1083821133305172 4.156624204406833 chrX 155270560 1862063 0.01199237640412967 0.40445778688744854 chrY 59373566 88637 0.0014928697393718948 0.20505839312798857