BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514726.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 71,669,416 number of mapped reads = 69,597,735 (97.11%) number of supplementary alignments = 2,004,682 (2.8%) number of secondary alignments = 0 number of mapped bases = 6,595,283,925 bp number of sequenced bases = 6,591,306,495 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,199,111 duplication rate = 49.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.5026 >>>>>>> ACTG content number of A's = 1,710,757,135 bp (25.95%) number of C's = 1,555,103,321 bp (23.59%) number of T's = 1,728,232,136 bp (26.22%) number of G's = 1,560,836,846 bp (23.68%) number of N's = 36,377,057 bp (0.55%) GC percentage = 47.27% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 59,025,943 number of insertions = 2,326,384 mapped reads with insertion percentage = 3.2% number of deletions = 1,839,819 mapped reads with deletion percentage = 2.56% homopolymer indels = 43.84% >>>>>>> Coverage mean coverageData = 2.1305X std coverageData = 43.2893X There is a 5.18% of reference with a coverageData >= 1X There is a 3.32% of reference with a coverageData >= 2X There is a 2.68% of reference with a coverageData >= 3X There is a 2.4% of reference with a coverageData >= 4X There is a 2.22% of reference with a coverageData >= 5X There is a 2.09% of reference with a coverageData >= 6X There is a 1.99% of reference with a coverageData >= 7X There is a 1.9% of reference with a coverageData >= 8X There is a 1.83% of reference with a coverageData >= 9X There is a 1.76% of reference with a coverageData >= 10X There is a 1.71% of reference with a coverageData >= 11X There is a 1.65% of reference with a coverageData >= 12X There is a 1.61% of reference with a coverageData >= 13X There is a 1.56% of reference with a coverageData >= 14X There is a 1.52% of reference with a coverageData >= 15X There is a 1.48% of reference with a coverageData >= 16X There is a 1.44% of reference with a coverageData >= 17X There is a 1.41% of reference with a coverageData >= 18X There is a 1.38% of reference with a coverageData >= 19X There is a 1.35% of reference with a coverageData >= 20X There is a 1.32% of reference with a coverageData >= 21X There is a 1.29% of reference with a coverageData >= 22X There is a 1.26% of reference with a coverageData >= 23X There is a 1.24% of reference with a coverageData >= 24X There is a 1.21% of reference with a coverageData >= 25X There is a 1.19% of reference with a coverageData >= 26X There is a 1.17% of reference with a coverageData >= 27X There is a 1.15% of reference with a coverageData >= 28X There is a 1.13% of reference with a coverageData >= 29X There is a 1.11% of reference with a coverageData >= 30X There is a 1.09% of reference with a coverageData >= 31X There is a 1.07% of reference with a coverageData >= 32X There is a 1.05% of reference with a coverageData >= 33X There is a 1.04% of reference with a coverageData >= 34X There is a 1.02% of reference with a coverageData >= 35X There is a 1% of reference with a coverageData >= 36X There is a 0.99% of reference with a coverageData >= 37X There is a 0.97% of reference with a coverageData >= 38X There is a 0.96% of reference with a coverageData >= 39X There is a 0.94% of reference with a coverageData >= 40X There is a 0.93% of reference with a coverageData >= 41X There is a 0.92% of reference with a coverageData >= 42X There is a 0.91% of reference with a coverageData >= 43X There is a 0.89% of reference with a coverageData >= 44X There is a 0.88% of reference with a coverageData >= 45X There is a 0.87% of reference with a coverageData >= 46X There is a 0.86% of reference with a coverageData >= 47X There is a 0.85% of reference with a coverageData >= 48X There is a 0.83% of reference with a coverageData >= 49X There is a 0.82% of reference with a coverageData >= 50X There is a 0.81% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 337655579 1.35468299996733 25.502935967577425 chr2 243199373 538024359 2.2122769165198464 69.22299849223404 chr3 198022430 692644876 3.497810202611896 39.077436734424026 chr4 191154276 409170128 2.140523019218257 26.22628598243421 chr5 180915260 102870503 0.5686115311665805 17.407363605901406 chr6 171115067 342381107 2.0008822893427616 36.8840136412408 chr7 159138663 165110599 1.0375266191597952 28.020313415740713 chr8 146364022 316893223 2.1651032724421855 30.20899756882772 chr9 141213431 20916963 0.14812304220552505 10.217874011331608 chr10 135534747 294720646 2.1745024986101904 51.00211867224218 chr11 135006516 108699546 0.8051429606553212 23.138011859026673 chr12 133851895 490749893 3.6663649252033377 37.64845987779194 chr13 115169878 141076013 1.2249384600372677 26.13056842908726 chr14 107349540 342886961 3.1941167237418995 33.779563566933334 chr15 102531392 817169719 7.969946599379047 79.71698954109215 chr16 90354753 321935964 3.5630219032307022 81.34908104877063 chr17 81195210 65597866 0.8079031509371057 13.295648203225266 chr18 78077248 597284316 7.649915068727832 97.98519689051595 chr19 59128983 124438407 2.104524730283286 79.76128060335301 chr20 63025520 88400345 1.4026119102230334 25.754129084832133 chr21 48129895 73958447 1.5366426001968216 21.326063205111534 chr22 51304566 49226589 0.9594972307143189 16.929372021503998 chrMT 16571 8310820 501.52797055096255 240.83465937242397 chrX 155270560 122502683 0.7889627177231795 22.368044275823657 chrY 59373566 22658373 0.3816239199781263 41.69495906968231