BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472738.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 = 23,540,284 number of mapped reads = 23,269,950 (98.85%) number of supplementary alignments = 82,650 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,691,499 number of mapped paired reads (second in pair) = 11,578,451 number of mapped paired reads (both in pair) = 23,105,300 number of mapped paired reads (singletons) = 164,650 number of mapped bases = 2,293,758,770 bp number of sequenced bases = 2,293,428,853 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,555,806 duplication rate = 49.05% >>>>>>> Insert size mean insert size = 23,194.5132 std insert size = 1,504,337.9613 median insert size = 253 >>>>>>> Mapping quality mean mapping quality = 55.3467 >>>>>>> ACTG content number of A's = 635,902,429 bp (27.73%) number of C's = 513,968,001 bp (22.41%) number of T's = 633,011,832 bp (27.6%) number of G's = 510,106,282 bp (22.24%) number of N's = 440,309 bp (0.02%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 15,147,956 number of insertions = 146,084 mapped reads with insertion percentage = 0.62% number of deletions = 138,582 mapped reads with deletion percentage = 0.59% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.741X std coverageData = 24.1515X There is a 6.09% of reference with a coverageData >= 1X There is a 2.67% of reference with a coverageData >= 2X There is a 1.21% of reference with a coverageData >= 3X There is a 0.83% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.54% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.45% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 273453937 1.0971043358002306 33.375955395383905 chr2 243199373 160537932 0.6601083301312624 26.20796304188599 chr3 198022430 282010037 1.4241317864849956 31.26486285086201 chr4 191154276 105186036 0.550267763824441 20.831867932139758 chr5 180915260 123306879 0.6815725716006489 25.88168510424906 chr6 171115067 127639203 0.745926149215136 18.221341935403274 chr7 159138663 113814614 0.7151914679589837 20.89155859860744 chr8 146364022 92193536 0.6298920645949453 22.448361765919415 chr9 141213431 127860825 0.9054437959233496 23.167343951843527 chr10 135534747 47067908 0.3472755809253844 11.330541674055022 chr11 135006516 91050827 0.6744180184606793 19.39007351564453 chr12 133851895 130740838 0.9767574676473576 32.93269278870449 chr13 115169878 60801733 0.5279308622693861 23.58189834435496 chr14 107349540 64946229 0.6049977391612484 24.480388770000083 chr15 102531392 50015877 0.4878103771379599 17.283229866510865 chr16 90354753 87385030 0.9671326310858268 29.076844847790426 chr17 81195210 78701981 0.9692933979726144 22.899022481619067 chr18 78077248 50418556 0.6457522170863399 32.64977717825433 chr19 59128983 47180364 0.7979228054708805 19.88832196305375 chr20 63025520 49956653 0.7926416632500612 20.557350534903545 chr21 48129895 10357901 0.2152072220394414 8.038633626917546 chr22 51304566 24853323 0.48442711707180214 16.77509259542817 chrMT 16571 10660 0.6432924989439383 1.3673821616495154 chrX 155270560 90697459 0.5841252778376017 16.99786154037218 chrY 59373566 3570432 0.06013504393520847 2.139457600642301