BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054607.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 = 13,647,369 number of mapped reads = 10,598,118 (77.66%) number of supplementary alignments = 309 (0%) number of secondary alignments = 0 number of mapped bases = 500,166,446 bp number of sequenced bases = 500,068,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,693,754 duplication rate = 11.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.849 >>>>>>> ACTG content number of A's = 148,720,451 bp (29.74%) number of C's = 96,922,783 bp (19.38%) number of T's = 149,472,182 bp (29.89%) number of G's = 104,949,385 bp (20.99%) number of N's = 3,819 bp (0%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 2,530,798 number of insertions = 19,940 mapped reads with insertion percentage = 0.19% number of deletions = 65,442 mapped reads with deletion percentage = 0.62% homopolymer indels = 46.81% >>>>>>> Coverage mean coverageData = 0.1616X std coverageData = 1.0217X There is a 8.35% of reference with a coverageData >= 1X There is a 2.75% of reference with a coverageData >= 2X There is a 1.41% of reference with a coverageData >= 3X There is a 0.86% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% 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 43854138 0.17594394679562303 1.1510400138767451 chr2 243199373 40705267 0.16737406226783322 1.151717514978133 chr3 198022430 36652688 0.18509361793004964 1.004934182298864 chr4 191154276 31864539 0.16669540261814494 1.0201225345315985 chr5 180915260 25533544 0.14113538017743776 0.7990298655698226 chr6 171115067 25197106 0.1472524099821087 0.9403152747446315 chr7 159138663 31417773 0.19742388435172414 1.2109324927860035 chr8 146364022 26222159 0.17915713603442793 1.0732368876259668 chr9 141213431 23213387 0.16438512141242428 1.0699264559698778 chr10 135534747 21454886 0.15829804883909215 1.0179714777514521 chr11 135006516 22418880 0.166057762723097 1.0262369350749108 chr12 133851895 19786193 0.14782153812615054 0.8410535813632648 chr13 115169878 15730533 0.13658547940807925 0.822831973969896 chr14 107349540 10826772 0.10085531805725484 0.8227516274793586 chr15 102531392 14365944 0.14011263984400016 0.8130286117853608 chr16 90354753 14091389 0.1559562561141637 1.0383032831701269 chr17 81195210 9675085 0.11915832227048861 0.7170433992788197 chr18 78077248 18810704 0.24092427028165747 1.3944063295423497 chr19 59128983 9488730 0.16047510913556554 1.0627641374118353 chr20 63025520 9402525 0.14918599640272703 0.9092761386687513 chr21 48129895 6173308 0.12826348364150805 1.0199459626633598 chr22 51304566 5093718 0.09928391168926368 0.6359675440892875 chrMT 16571 78669 4.747390018707381 8.109276627424986 chrX 155270560 36702725 0.23637916292695796 1.2745424158705219 chrY 59373566 1405784 0.023676933940602454 0.5129962351777464