BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089607.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 = 20,713,429 number of mapped reads = 17,606,419 (85%) number of supplementary alignments = 627 (0%) number of secondary alignments = 0 number of mapped bases = 825,795,826 bp number of sequenced bases = 825,634,979 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,383,967 duplication rate = 13.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4786 >>>>>>> ACTG content number of A's = 239,704,188 bp (29.03%) number of C's = 178,241,760 bp (21.59%) number of T's = 231,724,094 bp (28.07%) number of G's = 175,947,112 bp (21.31%) number of N's = 17,825 bp (0%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 3,663,423 number of insertions = 32,377 mapped reads with insertion percentage = 0.18% number of deletions = 108,435 mapped reads with deletion percentage = 0.61% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 0.2668X std coverageData = 1.6267X There is a 11.13% of reference with a coverageData >= 1X There is a 5.33% of reference with a coverageData >= 2X There is a 3.08% of reference with a coverageData >= 3X There is a 1.96% of reference with a coverageData >= 4X There is a 1.32% of reference with a coverageData >= 5X There is a 0.91% of reference with a coverageData >= 6X There is a 0.64% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 65139778 0.26134249029614254 2.5401302797916863 chr2 243199373 67131414 0.2760344863224627 1.9471390630203402 chr3 198022430 56293634 0.2842790788902045 1.1521251238726609 chr4 191154276 52243202 0.2733038626873301 1.2360467713971761 chr5 180915260 49591078 0.27411218932001646 1.1409568625966837 chr6 171115067 47421374 0.27713149304380075 1.4387867898071445 chr7 159138663 45293335 0.2846155305452076 2.1778635705107763 chr8 146364022 41855479 0.2859683577156687 1.78154590563904 chr9 141213431 34552091 0.24467991999996092 1.4317023787790404 chr10 135534747 37534643 0.27693741885982937 1.7447084564483815 chr11 135006516 37428678 0.27723608540494443 1.575326414920851 chr12 133851895 36536108 0.2729592136144206 1.1832117105841704 chr13 115169878 26985676 0.23431192659594552 1.054100766564045 chr14 107349540 26436068 0.2462615862163918 1.2790273629614926 chr15 102531392 24411899 0.23809194943925077 1.0832855093664213 chr16 90354753 23834450 0.2637874512257258 1.2493193216615874 chr17 81195210 22754546 0.2802449307046561 1.419507230035718 chr18 78077248 23321366 0.2986960554757258 2.308068670955069 chr19 59128983 16134455 0.2728688061487545 2.2297720155192544 chr20 63025520 17922981 0.28437656682562873 1.275562055450638 chr21 48129895 11004750 0.22864687321673982 1.2504801172897737 chr22 51304566 10169791 0.1982238968749877 1.0888568814174546 chrMT 16571 155103 9.359905859634301 11.078016086651028 chrX 155270560 49131214 0.316423242113637 1.5134456127447315 chrY 59373566 2512713 0.042320398946561505 0.7387239406124417