BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124951.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,557,026 number of mapped reads = 2,535,822 (99.17%) number of supplementary alignments = 33,790 (1.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,268,810 number of mapped paired reads (second in pair) = 1,267,012 number of mapped paired reads (both in pair) = 2,530,308 number of mapped paired reads (singletons) = 5,514 number of mapped bases = 340,751,080 bp number of sequenced bases = 340,490,004 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 408,820 duplication rate = 14.85% >>>>>>> Insert size mean insert size = 69,020.8242 std insert size = 2,505,811.1534 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.5864 >>>>>>> ACTG content number of A's = 100,281,416 bp (29.45%) number of C's = 67,841,941 bp (19.92%) number of T's = 99,909,149 bp (29.34%) number of G's = 72,427,809 bp (21.27%) number of N's = 29,689 bp (0.01%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 3,454,262 number of insertions = 71,062 mapped reads with insertion percentage = 2.63% number of deletions = 126,275 mapped reads with deletion percentage = 4.76% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.1101X std coverageData = 1.4918X There is a 6.2% of reference with a coverageData >= 1X There is a 3.38% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% 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 30279738 0.12148309953458451 1.659419161100327 chr2 243199373 32687537 0.13440633747028616 1.6837448761726834 chr3 198022430 24118115 0.12179486434945778 0.5019278262327432 chr4 191154276 22000042 0.1150905041747536 1.136925075639602 chr5 180915260 20331354 0.11238053661145002 0.47884530448648077 chr6 171115067 16256371 0.09500256923605681 0.9141026031711593 chr7 159138663 25051978 0.15742232294612152 2.4712496664251153 chr8 146364022 20182170 0.13789023917366797 0.619658985629965 chr9 141213431 13552732 0.09597339221932792 2.6442902856793165 chr10 135534747 18707877 0.13803011710347607 3.3824980379223004 chr11 135006516 15240437 0.11288667726230339 1.1998345491518645 chr12 133851895 14986948 0.11196664791335229 0.46813845870556103 chr13 115169878 9413452 0.08173536486684478 0.3945839131603932 chr14 107349540 10033870 0.09346914760883 0.46014049624988584 chr15 102531392 8166705 0.0796507766128836 0.3903133212849178 chr16 90354753 9316012 0.103104836111942 1.6019680070224658 chr17 81195210 7260176 0.08941630916405044 1.4302064961786451 chr18 78077248 8985524 0.11508505012881602 2.2774806315826317 chr19 59128983 4071682 0.06886101863108317 0.8978779905082198 chr20 63025520 7068634 0.11215510796261578 0.572256596591454 chr21 48129895 4579887 0.09515680431050182 0.6710826078972199 chr22 51304566 3304298 0.0644055345873114 0.36963948309234984 chrMT 16571 60557 3.654396234385372 3.413376059523452 chrX 155270560 10406893 0.06702425108790745 0.5220513844779998 chrY 59373566 4688091 0.07895922909531827 2.0154850345440525