BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236077.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 = 1,238,989 number of mapped reads = 1,060,584 (85.6%) number of supplementary alignments = 9,019 (0.73%) number of secondary alignments = 0 number of mapped bases = 69,229,981 bp number of sequenced bases = 69,187,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,668 duplication rate = 4.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3529 >>>>>>> ACTG content number of A's = 18,834,981 bp (27.22%) number of C's = 12,465,355 bp (18.02%) number of T's = 22,212,406 bp (32.1%) number of G's = 15,639,431 bp (22.6%) number of N's = 35,073 bp (0.05%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 594,143 number of insertions = 5,089 mapped reads with insertion percentage = 0.48% number of deletions = 24,524 mapped reads with deletion percentage = 2.28% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.2405X There is a 1.8% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 5092447 0.02043103034034166 0.30973979542604657 chr2 243199373 6085231 0.025021573554796953 0.2763455002878649 chr3 198022430 3934613 0.019869531951506706 0.16670796143497976 chr4 191154276 2624942 0.01373206006649833 0.15720439184637033 chr5 180915260 4681468 0.025876578902188793 0.19261215317048905 chr6 171115067 7224185 0.04221828694956476 0.29340785387500323 chr7 159138663 6353534 0.039924515389450015 0.4456387460603855 chr8 146364022 4147803 0.028338952041096547 0.317963753653321 chr9 141213431 2244715 0.015895902989567615 0.1964824244968911 chr10 135534747 1292945 0.00953958323322063 0.1821883799258668 chr11 135006516 3633471 0.026913300984672473 0.21978475094606356 chr12 133851895 1578503 0.011792907377217185 0.13109442196486834 chr13 115169878 3382669 0.02937112601612724 0.2052329913999559 chr14 107349540 2929425 0.02728865908507852 0.20320097048401495 chr15 102531392 2343325 0.02285470775623528 0.18257298185328147 chr16 90354753 2493979 0.02760207866430668 0.20617967254728703 chr17 81195210 1755523 0.02162101680628697 0.18512487870780223 chr18 78077248 2040379 0.026132824251182622 0.35420889092315794 chr19 59128983 772300 0.013061276565504263 0.22028202605376543 chr20 63025520 1113133 0.01766162341857711 0.16128521862238984 chr21 48129895 803627 0.01669704452918503 0.16570754584241423 chr22 51304566 732014 0.014268008816213356 0.13955107994832822 chrMT 16571 35924 2.167883652163418 2.0934981108292847 chrX 155270560 1780200 0.011465148319166235 0.13524560273779102 chrY 59373566 153626 0.0025874477541066 0.08904844413984575