BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779402.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 15,499,320 number of mapped reads = 14,888,106 (96.06%) number of supplementary alignments = 49,405 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,487,294 number of mapped paired reads (second in pair) = 7,400,812 number of mapped paired reads (both in pair) = 14,765,620 number of mapped paired reads (singletons) = 122,486 number of mapped bases = 1,182,744,974 bp number of sequenced bases = 1,182,466,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 522,742 duplication rate = 3.26% >>>>>>> Insert size mean insert size = 248,463.891 std insert size = 4,749,466.4311 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.9143 >>>>>>> ACTG content number of A's = 356,800,243 bp (30.17%) number of C's = 235,334,428 bp (19.9%) number of T's = 349,502,846 bp (29.56%) number of G's = 240,565,283 bp (20.34%) number of N's = 264,139 bp (0.02%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 3,672,992 number of insertions = 108,997 mapped reads with insertion percentage = 0.72% number of deletions = 131,461 mapped reads with deletion percentage = 0.87% homopolymer indels = 47.04% >>>>>>> Coverage mean coverageData = 0.3821X std coverageData = 1.2956X There is a 19.1% of reference with a coverageData >= 1X There is a 8.59% of reference with a coverageData >= 2X There is a 4.22% of reference with a coverageData >= 3X There is a 2.26% of reference with a coverageData >= 4X There is a 1.28% of reference with a coverageData >= 5X There is a 0.76% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.02% 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 0.01% 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% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 86097711 0.3454262647554246 1.5160651459785575 chr2 243199373 102257864 0.42046927481182284 1.076306695307495 chr3 198022430 75426411 0.38089832045794003 1.0342084110551415 chr4 191154276 73384524 0.3839020791771354 0.9734968335307901 chr5 180915260 82461423 0.4558013679995817 1.1210964779832007 chr6 171115067 45708731 0.267122771836334 1.0464663480426615 chr7 159138663 139082670 0.8739715879100982 3.0160851119778154 chr8 146364022 63733391 0.43544438127014573 1.0927847985615113 chr9 141213431 67743448 0.47972383023538323 1.5639370144987224 chr10 135534747 20225398 0.14922666288667658 1.3006619718580543 chr11 135006516 54474047 0.40349198404616266 1.06877377078574 chr12 133851895 64092546 0.4788318163145916 1.1401193746004419 chr13 115169878 41752513 0.3625298014121366 0.959298257611886 chr14 107349540 52000966 0.484407907104213 1.1906492173456242 chr15 102531392 31774706 0.3099022199952186 0.9783247672801151 chr16 90354753 14968362 0.16566214286480313 0.6567079592696443 chr17 81195210 31375155 0.3864163292391263 1.2780272093742966 chr18 78077248 29452743 0.3772256803928335 1.0555184994610645 chr19 59128983 15526420 0.26258560882063536 1.0762080585958096 chr20 63025520 24483268 0.38846594205014096 1.0628860346819813 chr21 48129895 17600564 0.3656888094187615 0.987325432983864 chr22 51304566 11623621 0.22656114077643694 0.8301769688918262 chrMT 16571 1114 0.0672258765312896 0.48780372035080277 chrX 155270560 32524326 0.20946872349787365 0.7630934161096669 chrY 59373566 4973052 0.0837586881677277 0.4157989997637539