BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927050.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 = 33,383,154 number of mapped reads = 32,465,735 (97.25%) number of supplementary alignments = 661,386 (1.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,332,554 number of mapped paired reads (second in pair) = 16,133,181 number of mapped paired reads (both in pair) = 31,932,692 number of mapped paired reads (singletons) = 533,043 number of mapped bases = 2,990,777,045 bp number of sequenced bases = 2,988,658,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,800,988 duplication rate = 6.89% >>>>>>> Insert size mean insert size = 216,006.4077 std insert size = 4,589,008.0149 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 53.1425 >>>>>>> ACTG content number of A's = 834,160,803 bp (27.91%) number of C's = 606,536,352 bp (20.29%) number of T's = 850,454,336 bp (28.46%) number of G's = 697,095,390 bp (23.32%) number of N's = 412,090 bp (0.01%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 31,473,280 number of insertions = 465,934 mapped reads with insertion percentage = 1.41% number of deletions = 1,469,515 mapped reads with deletion percentage = 4.42% homopolymer indels = 52.02% >>>>>>> Coverage mean coverageData = 0.9661X std coverageData = 3.2677X There is a 36.64% of reference with a coverageData >= 1X There is a 20.96% of reference with a coverageData >= 2X There is a 12.49% of reference with a coverageData >= 3X There is a 7.92% of reference with a coverageData >= 4X There is a 5.19% of reference with a coverageData >= 5X There is a 3.5% of reference with a coverageData >= 6X There is a 2.41% of reference with a coverageData >= 7X There is a 1.69% of reference with a coverageData >= 8X There is a 1.2% of reference with a coverageData >= 9X There is a 0.86% of reference with a coverageData >= 10X There is a 0.63% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% 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 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 0.01% 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 246475190 0.9888648983546564 3.9609704148523273 chr2 243199373 259834444 1.0684009617080714 5.933997376926235 chr3 198022430 202397994 1.022096304948889 1.977863854192988 chr4 191154276 166836736 0.8727857910957744 2.16365204528141 chr5 180915260 177080736 0.9788048614583424 1.9299555171864589 chr6 171115067 165520051 0.9673026104708827 1.9305683766899435 chr7 159138663 155661555 0.9781504510943391 2.311212738833331 chr8 146364022 149743287 1.0230880851306476 2.1856006229689733 chr9 141213431 128787586 0.9120066348363138 3.0578589089248815 chr10 135534747 146410493 1.080243230911111 3.3117175036103723 chr11 135006516 145337421 1.0765215287830996 3.193167279409072 chr12 133851895 137357005 1.0261864802138214 2.0088250000281818 chr13 115169878 87952420 0.7636755506504921 1.679982516535439 chr14 107349540 89480485 0.8335432550526066 1.8665429627614993 chr15 102531392 91398299 0.8914177133184732 1.9411921451792016 chr16 90354753 94481872 1.045676833403551 3.8527811195991384 chr17 81195210 81214496 1.000237526326984 2.3268581212714614 chr18 78077248 78433343 1.0045608036799658 2.960734638376439 chr19 59128983 54152293 0.9158333232283058 2.715874585713273 chr20 63025520 73193987 1.1613388830429325 2.258726547068239 chr21 48129895 36157981 0.7512582564329301 2.3782034643222496 chr22 51304566 41097312 0.8010458952133033 1.9864467412096578 chrMT 16571 7540533 455.04393217065956 344.6647513131686 chrX 155270560 169953635 1.0945644493070676 2.3272114226348064 chrY 59373566 4277891 0.07205043065798002 2.0392880959880064