BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975215.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 4,320,184 number of mapped reads = 4,275,464 (98.96%) number of supplementary alignments = 58,060 (1.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,145,220 number of mapped paired reads (second in pair) = 2,130,244 number of mapped paired reads (both in pair) = 4,257,764 number of mapped paired reads (singletons) = 17,700 number of mapped bases = 611,416,937 bp number of sequenced bases = 610,976,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 650,934 duplication rate = 12.9% >>>>>>> Insert size mean insert size = 60,547.8504 std insert size = 2,358,464.2772 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 53.6244 >>>>>>> ACTG content number of A's = 182,382,194 bp (29.85%) number of C's = 122,201,312 bp (20%) number of T's = 180,798,013 bp (29.59%) number of G's = 125,536,597 bp (20.55%) number of N's = 57,929 bp (0.01%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 5,266,074 number of insertions = 112,413 mapped reads with insertion percentage = 2.48% number of deletions = 220,478 mapped reads with deletion percentage = 4.95% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.1975X std coverageData = 2.5131X There is a 9.76% of reference with a coverageData >= 1X There is a 6.09% of reference with a coverageData >= 2X There is a 1.51% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 61719310 0.2476194833632932 2.703615779300924 chr2 243199373 55353065 0.22760365011302888 2.6881510328840643 chr3 198022430 50884084 0.2569612139392492 0.8323158458538876 chr4 191154276 27606276 0.14441882534712433 1.7781044153239 chr5 180915260 38231786 0.21132427413806884 0.7006280868374927 chr6 171115067 35155490 0.205449412587379 1.1361284349823921 chr7 159138663 31982021 0.20096952178114 2.7232639463403596 chr8 146364022 33779233 0.2307891826039052 1.0398386158908048 chr9 141213431 25883133 0.18329087266493793 3.463949683296552 chr10 135534747 27838735 0.20539924717607655 7.021180056072925 chr11 135006516 22291285 0.16511266019189771 2.4023157277703104 chr12 133851895 29725630 0.22207851446555912 0.7283440679627676 chr13 115169878 6728063 0.05841859969670195 0.34699514342231236 chr14 107349540 17870104 0.16646651676383523 0.638063894077351 chr15 102531392 11024176 0.10752000714083741 0.4837390096172941 chr16 90354753 17370677 0.19224973145574312 4.063587661506623 chr17 81195210 20451075 0.251875387722995 3.9279425103470302 chr18 78077248 23076370 0.2955581887312422 3.0399356429819373 chr19 59128983 12801083 0.21649421908710995 1.6737042402175042 chr20 63025520 16354805 0.2594949633101004 1.0281646535194602 chr21 48129895 10227782 0.21250372559507974 1.1189319415335737 chr22 51304566 3587763 0.06993067634564923 0.40253073269100337 chrMT 16571 147169 8.881117615110735 5.897727281557796 chrX 155270560 29516265 0.19009569489541353 1.0333215215907594 chrY 59373566 1811557 0.030511170577155498 2.359155497165525