BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231877.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 20,140,253 number of mapped reads = 8,080,600 (40.12%) number of supplementary alignments = 47,962 (0.24%) number of secondary alignments = 0 number of mapped bases = 515,317,052 bp number of sequenced bases = 515,116,355 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 609,318 duplication rate = 4.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.433 >>>>>>> ACTG content number of A's = 141,247,764 bp (27.42%) number of C's = 104,407,227 bp (20.27%) number of T's = 144,343,812 bp (28.02%) number of G's = 125,083,051 bp (24.28%) number of N's = 34,501 bp (0.01%) GC percentage = 44.55% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 3,541,018 number of insertions = 39,897 mapped reads with insertion percentage = 0.49% number of deletions = 125,210 mapped reads with deletion percentage = 1.53% homopolymer indels = 43.43% >>>>>>> Coverage mean coverageData = 0.1665X std coverageData = 18.1509X There is a 11.52% of reference with a coverageData >= 1X There is a 3% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% 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 39143031 0.15704286249300858 2.022465330721006 chr2 243199373 59478711 0.24456769878267737 64.64328944888113 chr3 198022430 34189432 0.1726543402179238 0.553498347231491 chr4 191154276 36636653 0.19166012796909654 0.6743888481891919 chr5 180915260 25839794 0.14282816164871887 0.5150286440689028 chr6 171115067 26203670 0.15313479087145493 0.7230552046484611 chr7 159138663 26001493 0.16338891197043676 1.6999930379408967 chr8 146364022 21267929 0.1453084488208448 1.1040432968241372 chr9 141213431 20306640 0.1438010524650449 1.0829076461472404 chr10 135534747 16752669 0.12360423707434964 1.204130567476474 chr11 135006516 21127292 0.1564909059648647 1.2581473865109876 chr12 133851895 24735731 0.18479925891224774 0.5940599416127993 chr13 115169878 18226272 0.15825554664562552 0.5296286642509972 chr14 107349540 13777200 0.12833962772453428 0.8180683826805389 chr15 102531392 17012276 0.16592260836564085 0.5678337447024681 chr16 90354753 16254339 0.17989467582297525 0.7844363665403742 chr17 81195210 15727545 0.19370040424798457 0.7533130995189459 chr18 78077248 10934466 0.1400467649679456 2.5012947038931643 chr19 59128983 12969415 0.21934108016029974 1.551799609706078 chr20 63025520 10317658 0.16370603526952257 0.6284231130160342 chr21 48129895 6767749 0.14061424817153664 0.6078990646117187 chr22 51304566 7019621 0.13682253934279456 0.5033550323244889 chrMT 16571 132220 7.978999456882506 10.070965261818301 chrX 155270560 32987200 0.2124498037490172 0.8388801520982462 chrY 59373566 1508046 0.025399282906470533 0.4623082269385232