BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054622.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 2,789,858 number of mapped reads = 2,056,756 (73.72%) number of supplementary alignments = 128 (0%) number of secondary alignments = 0 number of mapped bases = 94,003,801 bp number of sequenced bases = 93,986,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 480,605 duplication rate = 15.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.451 >>>>>>> ACTG content number of A's = 31,200,095 bp (33.2%) number of C's = 19,748,342 bp (21.01%) number of T's = 25,120,843 bp (26.73%) number of G's = 17,897,488 bp (19.04%) number of N's = 19,279 bp (0.02%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 604,911 number of insertions = 5,189 mapped reads with insertion percentage = 0.25% number of deletions = 11,921 mapped reads with deletion percentage = 0.58% homopolymer indels = 40.08% >>>>>>> Coverage mean coverageData = 0.0304X std coverageData = 0.7697X There is a 1.63% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8600045 0.03450360510837002 0.7935594477295953 chr2 243199373 7871665 0.0323671270320257 0.5790692823811834 chr3 198022430 6902528 0.03485730379129273 0.5203689419395057 chr4 191154276 5797393 0.03032834588539364 1.3161074410065288 chr5 180915260 4717436 0.026075390213075447 0.5212882029369614 chr6 171115067 4598437 0.02687336118683225 0.5860798040938828 chr7 159138663 6271850 0.03941122717613884 1.9837813616773607 chr8 146364022 4828006 0.03298628948581366 0.5608129022563321 chr9 141213431 4507125 0.03191711275678869 0.5321837453306052 chr10 135534747 4095019 0.030213794548198034 0.4995554183644723 chr11 135006516 4186481 0.031009473646442368 0.4318544760389408 chr12 133851895 3785634 0.028282259283665727 0.6052876130126029 chr13 115169878 2796478 0.024281331616935464 0.39500835400562717 chr14 107349540 1880780 0.017520149597287517 0.30998131247743715 chr15 102531392 2660277 0.025945975648121504 0.6831657999482971 chr16 90354753 2687509 0.029743969307292555 0.6170345865664358 chr17 81195210 1849201 0.022774754816201597 0.3691980479772067 chr18 78077248 3549794 0.04546515266521689 0.598598686179185 chr19 59128983 1818840 0.030760549356987927 0.4716285149463388 chr20 63025520 1833609 0.029093119739432533 0.5973270350439454 chr21 48129895 1045883 0.02173042347173207 0.5264830681616073 chr22 51304566 906786 0.01767456721103537 0.25081701429927394 chrMT 16571 7060 0.42604550117675455 1.6510890074395523 chrX 155270560 6499007 0.04185601571862689 0.6286402918027191 chrY 59373566 306958 0.005169943809674494 0.5680804960306197