BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617359.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 27,730,009 (86.66%) number of supplementary alignments = 60,720 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,390,366 number of mapped paired reads (second in pair) = 13,339,643 number of mapped paired reads (both in pair) = 26,318,536 number of mapped paired reads (singletons) = 1,411,473 number of mapped bases = 2,687,355,922 bp number of sequenced bases = 2,686,585,405 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,342,328 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 51,192.1693 std insert size = 2,157,253.0373 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.0841 >>>>>>> ACTG content number of A's = 815,416,571 bp (30.35%) number of C's = 533,398,425 bp (19.85%) number of T's = 804,846,169 bp (29.96%) number of G's = 532,173,801 bp (19.81%) number of N's = 750,439 bp (0.03%) GC percentage = 39.66% >>>>>>> Mismatches and indels general error rate = 0.0177 number of mismatches = 46,905,960 number of insertions = 274,988 mapped reads with insertion percentage = 0.96% number of deletions = 325,912 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.51% >>>>>>> Coverage mean coverageData = 0.8681X std coverageData = 8.4118X There is a 49.95% of reference with a coverageData >= 1X There is a 21.29% of reference with a coverageData >= 2X There is a 7.74% of reference with a coverageData >= 3X There is a 2.59% of reference with a coverageData >= 4X There is a 0.86% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 174521841 0.7001861832873829 17.464389831261393 chr2 243199373 264962550 1.0894869782415104 7.461555679605338 chr3 198022430 214937560 1.085420272844849 1.4021289772182972 chr4 191154276 147529877 0.7717843413557749 7.491643122948726 chr5 180915260 169659358 0.9377835678427568 1.3549721418141425 chr6 171115067 126676206 0.7402983747772486 3.3220016823744225 chr7 159138663 218705481 1.3743076438941806 9.796412006426957 chr8 146364022 113303182 0.7741190796191704 6.382710614574115 chr9 141213431 112853133 0.7991671344632933 12.097752980779138 chr10 135534747 112491203 0.8299805436608813 17.365901549273577 chr11 135006516 144276545 1.0686635673199656 4.7294452137564935 chr12 133851895 118890042 0.8882208354241081 1.2697544663602773 chr13 115169878 117831817 1.023113152902706 1.2209246563725156 chr14 107349540 77675355 0.7235741764706212 1.286093102587851 chr15 102531392 60597980 0.5910187974430309 0.9248291825557428 chr16 90354753 66977445 0.7412719616421286 7.203720805408568 chr17 81195210 82584903 1.0171154554560546 6.125712124906132 chr18 78077248 47996088 0.6147256624618737 12.794993065948685 chr19 59128983 49006117 0.8288002687277743 8.573196505288323 chr20 63025520 76330447 1.2111038036655628 2.0935005190643743 chr21 48129895 42764025 0.8885127424441711 2.746901252565513 chr22 51304566 23488141 0.45781775056824375 0.8469486731242198 chrMT 16571 1813964 109.46617584937542 21.28716401903147 chrX 155270560 112696524 0.7258074164220184 2.6406611653089658 chrY 59373566 8786138 0.1479806350186209 6.767450656857446