BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237852.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 = 1,659,744 number of mapped reads = 1,252,025 (75.43%) number of supplementary alignments = 4,675 (0.28%) number of secondary alignments = 0 number of mapped bases = 77,189,425 bp number of sequenced bases = 77,133,350 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,114 duplication rate = 5.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1074 >>>>>>> ACTG content number of A's = 20,106,795 bp (26.07%) number of C's = 13,289,269 bp (17.23%) number of T's = 24,902,644 bp (32.29%) number of G's = 18,770,614 bp (24.34%) number of N's = 64,028 bp (0.08%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 805,021 number of insertions = 7,052 mapped reads with insertion percentage = 0.56% number of deletions = 35,169 mapped reads with deletion percentage = 2.77% homopolymer indels = 49.28% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2672X There is a 1.9% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 6688223 0.026833325321985856 0.31361302203235303 chr2 243199373 6665476 0.027407455528267337 0.3622571500995052 chr3 198022430 5520327 0.02787728137666021 0.2365500347088583 chr4 191154276 4813208 0.025179703539564034 0.21620875706347784 chr5 180915260 4377534 0.024196599004417868 0.20496083017971548 chr6 171115067 4320247 0.025247613057943052 0.23508355472724507 chr7 159138663 4544510 0.028556919571455744 0.37396007579163415 chr8 146364022 4100400 0.02801508146585368 0.27892459089355914 chr9 141213431 3153433 0.022330970770053735 0.2549733798248117 chr10 135534747 3439914 0.02538031077742743 0.25298298571021477 chr11 135006516 3246357 0.02404592827208429 0.2781473248602116 chr12 133851895 4210323 0.031455086982519 0.24890323532117328 chr13 115169878 2634119 0.02287159668607099 0.2149023392989501 chr14 107349540 2172547 0.020238065295855017 0.19683382082501968 chr15 102531392 2333685 0.022760687770629312 0.20676561577504024 chr16 90354753 2013485 0.022284217854040285 0.22039448870163203 chr17 81195210 1791885 0.022068851105871885 0.21204309963368714 chr18 78077248 2056087 0.0263340096208309 0.4535990681046185 chr19 59128983 1351137 0.022850672063816826 0.2500965821468935 chr20 63025520 1560930 0.024766634214204025 0.21465043725092864 chr21 48129895 980468 0.02037128898785256 0.203206417562456 chr22 51304566 764323 0.014897757833094232 0.16165031921178283 chrMT 16571 49744 3.0018707380363283 3.1745530486888587 chrX 155270560 4151003 0.026733999027246377 0.23224816904722345 chrY 59373566 250060 0.004211638559826439 0.10356248351470407