BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008779.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 = 1,273,422 number of mapped reads = 1,170,248 (91.9%) number of supplementary alignments = 7,627 (0.6%) number of secondary alignments = 0 number of mapped bases = 78,423,570 bp number of sequenced bases = 78,391,075 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,848 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4211 >>>>>>> ACTG content number of A's = 21,509,257 bp (27.44%) number of C's = 14,727,036 bp (18.79%) number of T's = 24,556,461 bp (31.33%) number of G's = 17,476,061 bp (22.29%) number of N's = 122,260 bp (0.16%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 617,072 number of insertions = 5,646 mapped reads with insertion percentage = 0.48% number of deletions = 18,243 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.75% >>>>>>> Coverage mean coverageData = 0.0253X std coverageData = 0.2371X There is a 2.24% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% 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 6865075 0.027542860164027436 0.40798169918641686 chr2 243199373 6976760 0.02868740948604337 0.29894417797756995 chr3 198022430 5626716 0.02841453869644969 0.1904111405483905 chr4 191154276 5393378 0.02821479128199047 0.1933921509760061 chr5 180915260 4799399 0.026528436573012137 0.1795625933367881 chr6 171115067 3999125 0.02337096943076322 0.1855792306450182 chr7 159138663 4030949 0.025329790536194212 0.28148072531102325 chr8 146364022 4062826 0.027758365372058443 0.24141688721631807 chr9 141213431 2988278 0.02116142904282242 0.20173472313288748 chr10 135534747 3887318 0.02868133881564703 0.2773935047265112 chr11 135006516 3247197 0.02405215019399508 0.19406435423703708 chr12 133851895 4135985 0.030899711954022017 0.19465870700077662 chr13 115169878 2266552 0.019680076417203464 0.15471257369086208 chr14 107349540 2183940 0.020344195233626527 0.16194563370199802 chr15 102531392 2175406 0.021216975187462586 0.16066361935450849 chr16 90354753 2138346 0.023666115273426734 0.17878797234760482 chr17 81195210 2128869 0.026219145193417198 0.18714571261569385 chr18 78077248 2264702 0.029005914757651293 0.31731497240485523 chr19 59128983 1398557 0.02365264763643914 0.287643828937233 chr20 63025520 1528475 0.024251684079718817 0.17511253944415237 chr21 48129895 989863 0.020566489912350733 0.16591140580270605 chr22 51304566 970900 0.018924241557759205 0.15251423679235665 chrMT 16571 36087 2.17772011345121 1.9986536623332054 chrX 155270560 4127991 0.026585793211539907 0.18718497984288823 chrY 59373566 200876 0.003383256447827304 0.09108844914662372