BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975217.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 = 3,594,582 number of mapped reads = 3,557,576 (98.97%) number of supplementary alignments = 51,453 (1.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,785,882 number of mapped paired reads (second in pair) = 1,771,694 number of mapped paired reads (both in pair) = 3,540,418 number of mapped paired reads (singletons) = 17,158 number of mapped bases = 507,598,840 bp number of sequenced bases = 507,209,264 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 517,490 duplication rate = 12.08% >>>>>>> Insert size mean insert size = 113,196.1514 std insert size = 3,337,071.0471 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 53.7562 >>>>>>> ACTG content number of A's = 149,169,644 bp (29.41%) number of C's = 103,614,133 bp (20.43%) number of T's = 147,768,780 bp (29.13%) number of G's = 106,610,969 bp (21.02%) number of N's = 45,738 bp (0.01%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 4,660,326 number of insertions = 95,385 mapped reads with insertion percentage = 2.52% number of deletions = 192,566 mapped reads with deletion percentage = 5.19% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.164X std coverageData = 2.3125X There is a 8.51% of reference with a coverageData >= 1X There is a 4.97% of reference with a coverageData >= 2X There is a 1.11% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% 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 0.01% 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% 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 57556927 0.23091989407721475 2.252765145156435 chr2 243199373 44958938 0.18486453088018445 2.098126763326439 chr3 198022430 40024775 0.20212243128215324 0.7336916494284084 chr4 191154276 31871464 0.16673162990086604 1.87443566029861 chr5 180915260 22971119 0.12697170487442574 0.5253332479964868 chr6 171115067 28566245 0.1669417281647092 0.9269087103619302 chr7 159138663 25591999 0.16081572207251735 1.9837099256369741 chr8 146364022 27439880 0.18747694703278925 0.8052233119473406 chr9 141213431 26660304 0.18879439307724208 2.924172454926836 chr10 135534747 25010615 0.1845328637386249 7.336032150263026 chr11 135006516 19179658 0.14206468375200498 1.725913324860525 chr12 133851895 17469949 0.1305170091166808 0.5304298319281704 chr13 115169878 9253242 0.08034428932884691 0.40227187682475496 chr14 107349540 10117862 0.09425156363036115 0.4574153898844404 chr15 102531392 10130332 0.0988022478032874 0.4524751809449082 chr16 90354753 16903561 0.1870799314785355 4.186609872290127 chr17 81195210 13630755 0.16787634393703765 2.5989818418745934 chr18 78077248 18347782 0.2349952447094447 2.8141491616318186 chr19 59128983 8942602 0.15123889413081906 1.361747235532969 chr20 63025520 11136359 0.1766960272600686 0.9022189614921686 chr21 48129895 8249155 0.17139357981146644 1.1761162632725386 chr22 51304566 3596974 0.07011021202284412 0.3939569411345639 chrMT 16571 60783 3.66803451813409 3.128278488266485 chrX 155270560 25661894 0.1652721159761387 0.8350102398979404 chrY 59373566 4265666 0.07184453094833482 2.6582724463422838