BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230348.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 = 1,481,531 number of mapped reads = 355,028 (23.96%) number of supplementary alignments = 2,059 (0.14%) number of secondary alignments = 0 number of mapped bases = 22,479,536 bp number of sequenced bases = 22,469,300 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,259 duplication rate = 5.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1668 >>>>>>> ACTG content number of A's = 5,851,047 bp (26.04%) number of C's = 3,812,428 bp (16.97%) number of T's = 7,604,030 bp (33.84%) number of G's = 5,169,610 bp (23.01%) number of N's = 32,185 bp (0.14%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 253,090 number of insertions = 2,033 mapped reads with insertion percentage = 0.57% number of deletions = 6,465 mapped reads with deletion percentage = 1.8% homopolymer indels = 49.22% >>>>>>> Coverage mean coverageData = 0.0073X std coverageData = 0.1143X There is a 0.57% of reference with a coverageData >= 1X There is a 0.1% 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% 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 1919787 0.007702235574369943 0.13048982271521764 chr2 243199373 1887544 0.007761302904345893 0.1253408843520723 chr3 198022430 1504637 0.007598316008949087 0.11021299225718832 chr4 191154276 1595406 0.008346169562013879 0.11646501001507034 chr5 180915260 1400781 0.0077427465212166185 0.11005822055665003 chr6 171115067 1266134 0.007399313352108263 0.11557968020474772 chr7 159138663 1192728 0.007494897704400093 0.12435132970164667 chr8 146364022 1213513 0.008291060763552944 0.12716919591002765 chr9 141213431 914364 0.006475049813073375 0.10419476971471514 chr10 135534747 1021527 0.007537011892603452 0.11268392686816874 chr11 135006516 943005 0.006984885085102114 0.11081933797832225 chr12 133851895 1019198 0.007614371092766374 0.1101740771589865 chr13 115169878 741853 0.006441380444980588 0.10399402757791547 chr14 107349540 643419 0.005993681947775463 0.09840333859273612 chr15 102531392 584340 0.005699132612965988 0.09353138121718117 chr16 90354753 587998 0.006507659868208593 0.10160678700410475 chr17 81195210 560721 0.006905838410911185 0.10513734777323358 chr18 78077248 594333 0.007612115119631266 0.13180251918032998 chr19 59128983 444594 0.0075190537270022045 0.11798294986335171 chr20 63025520 461377 0.007320479069430922 0.10664337784137243 chr21 48129895 311424 0.006470489910688565 0.10528711309502299 chr22 51304566 233860 0.004558268751362208 0.08348795630604955 chrMT 16571 60761 3.6667068975921793 4.25590890544284 chrX 155270560 1294989 0.008340209502690014 0.11648268625223868 chrY 59373566 81243 0.0013683362053746274 0.044841870015541935