BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819143.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,258,149 number of mapped reads = 1,134,220 (90.15%) number of supplementary alignments = 5,028 (0.4%) number of secondary alignments = 0 number of mapped bases = 66,012,936 bp number of sequenced bases = 65,992,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,237 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.773 >>>>>>> ACTG content number of A's = 16,156,492 bp (24.48%) number of C's = 13,536,160 bp (20.51%) number of T's = 21,169,857 bp (32.08%) number of G's = 15,129,070 bp (22.93%) number of N's = 887 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 346,273 number of insertions = 4,414 mapped reads with insertion percentage = 0.39% number of deletions = 12,279 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.2259X There is a 1.87% of reference with a coverageData >= 1X There is a 0.19% 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 6394496 0.02565488492804999 0.40155931355236907 chr2 243199373 5136707 0.02112138257856446 0.27163515578673303 chr3 198022430 3608066 0.018220491486747235 0.1503433066945231 chr4 191154276 3609763 0.018884029567824055 0.1852048676500265 chr5 180915260 3562153 0.019689621538835363 0.15553622436812228 chr6 171115067 2773365 0.01620760257189976 0.17163668040870522 chr7 159138663 3522616 0.022135513354162088 0.25662234751143503 chr8 146364022 5928206 0.040503164090421075 0.2612970368508733 chr9 141213431 2784751 0.01972015678876891 0.18693234216820537 chr10 135534747 3464616 0.025562566623598005 0.2473298191520667 chr11 135006516 2288407 0.016950344826319345 0.18852287601742232 chr12 133851895 3066486 0.022909544911560647 0.16901228602862856 chr13 115169878 1390243 0.012071237932543439 0.12258770963735155 chr14 107349540 1595728 0.014864786565457104 0.13791177892319487 chr15 102531392 1766866 0.017232439407435334 0.145631740787137 chr16 90354753 2110611 0.023359158538123613 0.17816652957348053 chr17 81195210 2395826 0.029506986926938178 0.20083431426752205 chr18 78077248 1567027 0.020070213028000168 0.3256253862407105 chr19 59128983 1424705 0.024094867317437204 0.28436252863753303 chr20 63025520 1985757 0.03150718946864699 0.20261306577340515 chr21 48129895 926221 0.019244193239981097 0.1767826595345588 chr22 51304566 559839 0.01091206969765615 0.11723061548399102 chrMT 16571 10531 0.6355078148572808 0.9500997156404837 chrX 155270560 3873643 0.024947697747725005 0.18476554796843234 chrY 59373566 266307 0.004485278852882106 0.16755560070745482