BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472559.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 12,862,610 number of mapped reads = 12,592,838 (97.9%) number of supplementary alignments = 59,741 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,322,322 number of mapped paired reads (second in pair) = 6,270,516 number of mapped paired reads (both in pair) = 12,474,656 number of mapped paired reads (singletons) = 118,182 number of mapped bases = 1,233,155,808 bp number of sequenced bases = 1,233,007,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,695,276 duplication rate = 46.72% >>>>>>> Insert size mean insert size = 32,235.0038 std insert size = 1,775,532.6371 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 54.9114 >>>>>>> ACTG content number of A's = 335,360,886 bp (27.2%) number of C's = 283,364,293 bp (22.98%) number of T's = 332,013,574 bp (26.93%) number of G's = 282,078,905 bp (22.88%) number of N's = 189,411 bp (0.02%) GC percentage = 45.86% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 7,991,734 number of insertions = 75,290 mapped reads with insertion percentage = 0.59% number of deletions = 61,428 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.84% >>>>>>> Coverage mean coverageData = 0.3983X std coverageData = 14.2124X There is a 3.57% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 165388795 0.6635441642490432 23.573938813104178 chr2 243199373 70445124 0.28965997375330405 9.434529721743132 chr3 198022430 130968606 0.6613826827597258 16.40284263068026 chr4 191154276 50068827 0.2619288882661458 10.254780690550419 chr5 180915260 54360698 0.3004760239683485 9.189835551667521 chr6 171115067 81240678 0.47477220693838723 15.414668548013582 chr7 159138663 54817512 0.34446382146618887 10.952998443791428 chr8 146364022 58259122 0.39804264192739935 13.976779161153631 chr9 141213431 59580606 0.4219188329189452 10.265100972983532 chr10 135534747 40135632 0.29612798849286964 12.031822455240803 chr11 135006516 43286238 0.3206233245808669 9.991459361858086 chr12 133851895 70279201 0.5250519688197167 20.37616131671711 chr13 115169878 28644879 0.2487184973834912 11.71848485283564 chr14 107349540 26084931 0.24299061737945035 8.163984571576558 chr15 102531392 30015815 0.2927475616443401 9.85449363047758 chr16 90354753 41647515 0.4609333058549781 13.57941359234533 chr17 81195210 73007366 0.899158534105645 25.304899004615457 chr18 78077248 20673525 0.26478296212489455 10.0478673603062 chr19 59128983 32560689 0.550672231247407 20.068413870773618 chr20 63025520 27823376 0.44146206171722185 12.319249751002664 chr21 48129895 6819739 0.14169444998789213 6.08871170278303 chr22 51304566 12690699 0.24736003029437964 13.988899249603795 chrMT 16571 3319 0.20028966266368958 0.5801952714313716 chrX 155270560 52477311 0.337973347941812 13.831516104291225 chrY 59373566 1875605 0.03158989978806393 1.4563317812061813