BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240196.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 = 1,708,504 number of mapped reads = 1,306,076 (76.45%) number of supplementary alignments = 6,736 (0.39%) number of secondary alignments = 0 number of mapped bases = 80,095,281 bp number of sequenced bases = 80,052,035 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,455 duplication rate = 9.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6587 >>>>>>> ACTG content number of A's = 21,337,063 bp (26.65%) number of C's = 13,574,389 bp (16.96%) number of T's = 26,644,610 bp (33.28%) number of G's = 18,477,042 bp (23.08%) number of N's = 18,931 bp (0.02%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 744,448 number of insertions = 5,601 mapped reads with insertion percentage = 0.43% number of deletions = 25,547 mapped reads with deletion percentage = 1.93% homopolymer indels = 49.52% >>>>>>> Coverage mean coverageData = 0.0259X std coverageData = 0.2721X There is a 1.85% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 5937752 0.02382241607333849 0.35558909884907774 chr2 243199373 8062827 0.033153157019035574 0.332371364252632 chr3 198022430 5637989 0.028471466590931138 0.22678692856256266 chr4 191154276 5544721 0.029006523505652575 0.2330992141391912 chr5 180915260 4509109 0.024923873198977244 0.21165778186438877 chr6 171115067 4587182 0.02680758673343476 0.24721801712237063 chr7 159138663 4744618 0.029814363841928218 0.4246171559053485 chr8 146364022 4876436 0.033317176812755256 0.3814237157666264 chr9 141213431 2964123 0.02099037590836526 0.24049280023054273 chr10 135534747 3707058 0.027351347769144396 0.24879715154250256 chr11 135006516 3708732 0.027470762966729696 0.2602555067482152 chr12 133851895 3485618 0.026040856575097422 0.21766928407098501 chr13 115169878 2221212 0.0192863970907393 0.18691009491211638 chr14 107349540 2651740 0.024701922337068236 0.22030348349466952 chr15 102531392 2027608 0.019775484955866004 0.1938472134818206 chr16 90354753 2066314 0.022868902093064213 0.2019914861801422 chr17 81195210 2088916 0.025727084146958915 0.2233153655204408 chr18 78077248 1883607 0.024124915365869453 0.33695155926422143 chr19 59128983 1368403 0.023142677762612626 0.27333058360359525 chr20 63025520 1522356 0.02415459642379785 0.20953997779012423 chr21 48129895 1185672 0.024634834545140812 0.21255863332197725 chr22 51304566 702645 0.013695564640386978 0.1504627255078704 chrMT 16571 51235 3.0918472029449036 3.4510183286393086 chrX 155270560 4384693 0.028239049308510254 0.2374384039654418 chrY 59373566 174715 0.002942639490442599 0.07461244161955949