BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975210.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 76,468,628 number of mapped reads = 76,394,166 (99.9%) number of supplementary alignments = 563,380 (0.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 38,199,533 number of mapped paired reads (second in pair) = 38,194,633 number of mapped paired reads (both in pair) = 76,361,418 number of mapped paired reads (singletons) = 32,748 number of mapped bases = 7,472,221,086 bp number of sequenced bases = 7,471,304,401 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,443,720 duplication rate = 60.81% >>>>>>> Insert size mean insert size = 102,621.393 std insert size = 3,218,840.0421 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 56.0756 >>>>>>> ACTG content number of A's = 1,879,790,352 bp (25.16%) number of C's = 1,835,749,386 bp (24.57%) number of T's = 1,934,886,769 bp (25.9%) number of G's = 1,820,607,807 bp (24.37%) number of N's = 270,087 bp (0%) GC percentage = 48.94% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 29,487,243 number of insertions = 610,480 mapped reads with insertion percentage = 0.79% number of deletions = 406,842 mapped reads with deletion percentage = 0.52% homopolymer indels = 33.02% >>>>>>> Coverage mean coverageData = 2.4137X std coverageData = 21.591X There is a 9.52% of reference with a coverageData >= 1X There is a 6.62% of reference with a coverageData >= 2X There is a 4.86% of reference with a coverageData >= 3X There is a 4.05% of reference with a coverageData >= 4X There is a 3.54% of reference with a coverageData >= 5X There is a 3.28% of reference with a coverageData >= 6X There is a 3.07% of reference with a coverageData >= 7X There is a 2.94% of reference with a coverageData >= 8X There is a 2.83% of reference with a coverageData >= 9X There is a 2.74% of reference with a coverageData >= 10X There is a 2.66% of reference with a coverageData >= 11X There is a 2.59% of reference with a coverageData >= 12X There is a 2.53% of reference with a coverageData >= 13X There is a 2.47% of reference with a coverageData >= 14X There is a 2.42% of reference with a coverageData >= 15X There is a 2.37% of reference with a coverageData >= 16X There is a 2.32% of reference with a coverageData >= 17X There is a 2.27% of reference with a coverageData >= 18X There is a 2.23% of reference with a coverageData >= 19X There is a 2.19% of reference with a coverageData >= 20X There is a 2.15% of reference with a coverageData >= 21X There is a 2.11% of reference with a coverageData >= 22X There is a 2.08% of reference with a coverageData >= 23X There is a 2.04% of reference with a coverageData >= 24X There is a 2.01% of reference with a coverageData >= 25X There is a 1.97% of reference with a coverageData >= 26X There is a 1.94% of reference with a coverageData >= 27X There is a 1.91% of reference with a coverageData >= 28X There is a 1.88% of reference with a coverageData >= 29X There is a 1.85% of reference with a coverageData >= 30X There is a 1.82% of reference with a coverageData >= 31X There is a 1.79% of reference with a coverageData >= 32X There is a 1.76% of reference with a coverageData >= 33X There is a 1.74% of reference with a coverageData >= 34X There is a 1.71% of reference with a coverageData >= 35X There is a 1.69% of reference with a coverageData >= 36X There is a 1.66% of reference with a coverageData >= 37X There is a 1.64% of reference with a coverageData >= 38X There is a 1.61% of reference with a coverageData >= 39X There is a 1.59% of reference with a coverageData >= 40X There is a 1.57% of reference with a coverageData >= 41X There is a 1.54% of reference with a coverageData >= 42X There is a 1.52% of reference with a coverageData >= 43X There is a 1.5% of reference with a coverageData >= 44X There is a 1.48% of reference with a coverageData >= 45X There is a 1.46% of reference with a coverageData >= 46X There is a 1.44% of reference with a coverageData >= 47X There is a 1.42% of reference with a coverageData >= 48X There is a 1.4% of reference with a coverageData >= 49X There is a 1.38% of reference with a coverageData >= 50X There is a 1.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 974626696 3.9102277542570296 32.12089998457127 chr2 243199373 442954413 1.8213633017877888 15.561168387790593 chr3 198022430 487643991 2.462569472559245 20.764283376193546 chr4 191154276 255525676 1.3367510334950603 13.313059355912943 chr5 180915260 489029546 2.7030862183764928 24.774032581372587 chr6 171115067 418914984 2.4481478536311476 23.63691977929156 chr7 159138663 307208652 1.9304463554529172 17.23968575637432 chr8 146364022 286015797 1.954140048160196 19.465538666955045 chr9 141213431 259598689 1.8383427635859935 16.20894577942769 chr10 135534747 265246948 1.9570401972270624 17.38438533553415 chr11 135006516 389505396 2.8850859020760153 21.580690874695083 chr12 133851895 356307888 2.6619562464916915 20.385022708323827 chr13 115169878 87881420 0.7630590700113444 9.027843724998903 chr14 107349540 252170360 2.3490585986674932 21.802527028662347 chr15 102531392 223088249 2.1758043526805917 17.66789148343204 chr16 90354753 253283349 2.8032100203959387 21.489371845634683 chr17 81195210 326202193 4.0175053799355895 24.66562826863597 chr18 78077248 100237570 1.2838256030745345 13.275224822232184 chr19 59128983 457793915 7.74229306463803 41.32563644804419 chr20 63025520 165797454 2.6306400010662347 21.956871592513814 chr21 48129895 70631467 1.4675175792509 14.912003909645076 chr22 51304566 139966441 2.728147841656043 20.1461580028027 chrMT 16571 3452787 208.3632249109891 279.43201186637395 chrX 155270560 457441703 2.946094243493422 29.572298534214546 chrY 59373566 1695502 0.02855651284276912 1.0009764652168311