BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163053.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 69,617,632 number of mapped reads = 68,832,134 (98.87%) number of supplementary alignments = 357,362 (0.51%) number of secondary alignments = 0 number of mapped bases = 6,712,871,261 bp number of sequenced bases = 6,712,041,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,919,861 duplication rate = 46.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0611 >>>>>>> ACTG content number of A's = 1,621,566,300 bp (24.16%) number of C's = 1,733,784,155 bp (25.83%) number of T's = 1,617,316,515 bp (24.1%) number of G's = 1,738,889,857 bp (25.91%) number of N's = 484,384 bp (0.01%) GC percentage = 51.74% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 24,958,056 number of insertions = 454,405 mapped reads with insertion percentage = 0.65% number of deletions = 378,423 mapped reads with deletion percentage = 0.54% homopolymer indels = 47% >>>>>>> Coverage mean coverageData = 2.1685X std coverageData = 33.587X There is a 7.09% of reference with a coverageData >= 1X There is a 4.86% of reference with a coverageData >= 2X There is a 3.71% of reference with a coverageData >= 3X There is a 3.28% of reference with a coverageData >= 4X There is a 2.96% of reference with a coverageData >= 5X There is a 2.75% of reference with a coverageData >= 6X There is a 2.57% of reference with a coverageData >= 7X There is a 2.44% of reference with a coverageData >= 8X There is a 2.32% of reference with a coverageData >= 9X There is a 2.21% of reference with a coverageData >= 10X There is a 2.12% of reference with a coverageData >= 11X There is a 2.04% of reference with a coverageData >= 12X There is a 1.97% of reference with a coverageData >= 13X There is a 1.9% of reference with a coverageData >= 14X There is a 1.84% of reference with a coverageData >= 15X There is a 1.78% of reference with a coverageData >= 16X There is a 1.73% of reference with a coverageData >= 17X There is a 1.68% of reference with a coverageData >= 18X There is a 1.64% of reference with a coverageData >= 19X There is a 1.59% of reference with a coverageData >= 20X There is a 1.55% of reference with a coverageData >= 21X There is a 1.52% of reference with a coverageData >= 22X There is a 1.48% of reference with a coverageData >= 23X There is a 1.45% of reference with a coverageData >= 24X There is a 1.41% of reference with a coverageData >= 25X There is a 1.38% of reference with a coverageData >= 26X There is a 1.35% of reference with a coverageData >= 27X There is a 1.32% of reference with a coverageData >= 28X There is a 1.3% of reference with a coverageData >= 29X There is a 1.27% of reference with a coverageData >= 30X There is a 1.25% of reference with a coverageData >= 31X There is a 1.22% of reference with a coverageData >= 32X There is a 1.2% of reference with a coverageData >= 33X There is a 1.18% of reference with a coverageData >= 34X There is a 1.15% of reference with a coverageData >= 35X There is a 1.13% of reference with a coverageData >= 36X There is a 1.11% of reference with a coverageData >= 37X There is a 1.09% of reference with a coverageData >= 38X There is a 1.08% of reference with a coverageData >= 39X There is a 1.06% of reference with a coverageData >= 40X There is a 1.04% of reference with a coverageData >= 41X There is a 1.02% of reference with a coverageData >= 42X There is a 1.01% of reference with a coverageData >= 43X There is a 0.99% of reference with a coverageData >= 44X There is a 0.97% of reference with a coverageData >= 45X There is a 0.96% of reference with a coverageData >= 46X There is a 0.95% of reference with a coverageData >= 47X There is a 0.93% of reference with a coverageData >= 48X There is a 0.92% of reference with a coverageData >= 49X There is a 0.9% of reference with a coverageData >= 50X There is a 0.89% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 704159988 2.8251082592087102 38.63887848639966 chr2 243199373 181451835 0.7461032187776241 14.136398945250921 chr3 198022430 355633645 1.7959260726171273 25.25602759928139 chr4 191154276 224656201 1.175261185368409 19.677039760921737 chr5 180915260 418535169 2.3134320952251346 38.866890617507956 chr6 171115067 267958723 1.565956333932885 26.734597583533294 chr7 159138663 378012659 2.3753665631839573 42.649129906454256 chr8 146364022 461138338 3.150626306238018 59.600126482287884 chr9 141213431 285564716 2.0222206484027714 31.890619408788034 chr10 135534747 229944187 1.6965700094603784 22.725563464692144 chr11 135006516 446279808 3.3056168044511276 35.46362472060674 chr12 133851895 233922329 1.7476205996187055 23.26754545090708 chr13 115169878 135145369 1.1734437106896995 19.083171857017426 chr14 107349540 100545435 0.936617287787167 16.148827287415436 chr15 102531392 253252004 2.4699947894982253 27.874464471673132 chr16 90354753 401500660 4.443603094128319 42.718241422716744 chr17 81195210 235368266 2.8987949658606706 32.82538568193626 chr18 78077248 124938234 1.6001874707469197 23.716909966815663 chr19 59128983 473567141 8.009052700940249 68.70413451882487 chr20 63025520 214352170 3.401037706630584 36.63381496141295 chr21 48129895 121829891 2.5312727359991123 47.96313014071351 chr22 51304566 119668971 2.332520871534124 30.009703928221196 chrMT 16571 2482 0.14977973568281938 0.4766116791036192 chrX 155270560 335743685 2.1623138668399213 38.795236341243665 chrY 59373566 9699355 0.16336150333298155 9.776550601639238