BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053639.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 = 14,548,560 number of mapped reads = 10,036,248 (68.98%) number of supplementary alignments = 230 (0%) number of secondary alignments = 0 number of mapped bases = 472,323,853 bp number of sequenced bases = 472,229,824 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,167,718 duplication rate = 20.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8862 >>>>>>> ACTG content number of A's = 140,864,153 bp (29.83%) number of C's = 94,495,816 bp (20.01%) number of T's = 137,854,442 bp (29.19%) number of G's = 99,014,416 bp (20.97%) number of N's = 997 bp (0%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 2,661,031 number of insertions = 19,617 mapped reads with insertion percentage = 0.2% number of deletions = 63,693 mapped reads with deletion percentage = 0.63% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.1526X std coverageData = 1.3731X There is a 5.26% of reference with a coverageData >= 1X There is a 2.23% of reference with a coverageData >= 2X There is a 1.43% of reference with a coverageData >= 3X There is a 1.03% of reference with a coverageData >= 4X There is a 0.79% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.5% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% 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 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 37625191 0.15095324877846544 1.4157444315428174 chr2 243199373 40565237 0.16679827953339338 1.6019228582430316 chr3 198022430 32355791 0.16339457605888383 1.3345999937158257 chr4 191154276 31156549 0.16299164032302368 1.3887860668385226 chr5 180915260 29379056 0.16239125433642249 1.3220786712245791 chr6 171115067 28509259 0.16660870079897758 1.4696770992188903 chr7 159138663 25536185 0.1604649964917702 1.4936539181258544 chr8 146364022 24015456 0.16408032296352174 1.462474644919017 chr9 141213431 19040311 0.1348335697615052 1.2456444605794794 chr10 135534747 21973095 0.16212148903778895 1.4157161549870996 chr11 135006516 21863250 0.16194218359060536 1.484288400215702 chr12 133851895 21406569 0.15992727633777618 1.3145288849404515 chr13 115169878 15421751 0.1339043790599483 1.1947823659719041 chr14 107349540 14308801 0.13329168434256913 1.3399085709072804 chr15 102531392 13708355 0.13369910163708693 1.1991415901748428 chr16 90354753 13069878 0.14465069701424563 1.3162366106076324 chr17 81195210 12328887 0.15184254095777325 1.2367240497202834 chr18 78077248 12188479 0.15610794837440992 1.4460523830783047 chr19 59128983 8615619 0.1457088987984116 1.3743532111245753 chr20 63025520 10106671 0.16035839133100369 1.3299353983374562 chr21 48129895 5953792 0.12370257612238714 1.202945586897194 chr22 51304566 5232928 0.10199731540463669 0.9637218780704172 chrMT 16571 80382 4.850763381811599 9.617970791627304 chrX 155270560 26726444 0.1721282128434392 1.4250984031657845 chrY 59373566 1155917 0.019468545985599047 0.41175324824375076