BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927061.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 32,802,858 number of mapped reads = 32,328,032 (98.55%) number of supplementary alignments = 268,982 (0.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,217,252 number of mapped paired reads (second in pair) = 16,110,780 number of mapped paired reads (both in pair) = 32,055,272 number of mapped paired reads (singletons) = 272,760 number of mapped bases = 3,085,176,364 bp number of sequenced bases = 3,082,841,691 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,147,961 duplication rate = 5.19% >>>>>>> Insert size mean insert size = 83,402.8696 std insert size = 2,814,293.8816 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.7056 >>>>>>> ACTG content number of A's = 892,587,662 bp (28.95%) number of C's = 614,594,892 bp (19.94%) number of T's = 902,564,208 bp (29.28%) number of G's = 672,551,242 bp (21.82%) number of N's = 543,687 bp (0.02%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 31,305,819 number of insertions = 503,201 mapped reads with insertion percentage = 1.53% number of deletions = 1,665,141 mapped reads with deletion percentage = 5.01% homopolymer indels = 53.09% >>>>>>> Coverage mean coverageData = 0.9966X std coverageData = 3.8337X There is a 35.53% of reference with a coverageData >= 1X There is a 21.26% of reference with a coverageData >= 2X There is a 13.16% of reference with a coverageData >= 3X There is a 8.58% of reference with a coverageData >= 4X There is a 5.74% of reference with a coverageData >= 5X There is a 3.93% of reference with a coverageData >= 6X There is a 2.74% of reference with a coverageData >= 7X There is a 1.94% of reference with a coverageData >= 8X There is a 1.38% of reference with a coverageData >= 9X There is a 1% of reference with a coverageData >= 10X There is a 0.73% of reference with a coverageData >= 11X There is a 0.54% of reference with a coverageData >= 12X There is a 0.4% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% 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 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 257031421 1.031216772775864 4.566895956149219 chr2 243199373 274062945 1.1269064620491436 6.484290959211832 chr3 198022430 213624046 1.078787115176801 2.123499575756036 chr4 191154276 191626354 1.0024696177866301 3.097167577531927 chr5 180915260 188353094 1.041112253327884 2.034503366033008 chr6 171115067 176742900 1.0328891727576508 2.06575064794229 chr7 159138663 160427604 1.0080994836559611 2.656647309990949 chr8 146364022 155104628 1.0597182687423006 2.4001884000617966 chr9 141213431 136116537 0.963906450229936 5.114291754532523 chr10 135534747 148797266 1.0978532759573454 8.342288843944816 chr11 135006516 144324660 1.0690199575256056 2.787530768230774 chr12 133851895 133652117 0.9985074697672379 2.02712889326093 chr13 115169878 95557450 0.8297087021312985 1.8234866651320438 chr14 107349540 91929552 0.8563572046978497 1.9482951996378515 chr15 102531392 86702991 0.845623855374947 1.8973569762108196 chr16 90354753 93750744 1.037585084206915 5.01073387404954 chr17 81195210 78556832 0.9675057432575148 2.644782543817846 chr18 78077248 84795383 1.0860447207360586 5.064602094669642 chr19 59128983 44719417 0.756302826990953 2.7419673980606767 chr20 63025520 72806618 1.1551926584659675 2.419260955795731 chr21 48129895 39745366 0.8257937400445191 2.7561602353534425 chr22 51304566 36850990 0.718278953962889 1.8564362893477806 chrMT 16571 223317 13.476374388992818 10.191741486707656 chrX 155270560 174593575 1.1244473839728535 2.36507792514522 chrY 59373566 5080557 0.08556934242420272 3.8251102913393447