BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094065.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 394,518 number of mapped reads = 368,403 (93.38%) number of supplementary alignments = 13,417 (3.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 185,004 number of mapped paired reads (second in pair) = 183,399 number of mapped paired reads (both in pair) = 365,634 number of mapped paired reads (singletons) = 2,769 number of mapped bases = 47,982,662 bp number of sequenced bases = 46,895,840 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 351,471 duplication rate = 49.47% >>>>>>> Insert size mean insert size = 341,548.2895 std insert size = 5,272,061.2878 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 37.7301 >>>>>>> ACTG content number of A's = 12,453,668 bp (26.56%) number of C's = 10,997,578 bp (23.45%) number of T's = 11,783,489 bp (25.13%) number of G's = 11,660,571 bp (24.86%) number of N's = 534 bp (0%) GC percentage = 48.32% >>>>>>> Mismatches and indels general error rate = 0.0418 number of mismatches = 1,891,291 number of insertions = 32,248 mapped reads with insertion percentage = 8.6% number of deletions = 154,174 mapped reads with deletion percentage = 39.9% homopolymer indels = 27.26% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 4.2175X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 333552 0.001338219333864769 0.6035897863822172 chr2 243199373 1675943 0.006891230759875355 2.6281301369988297 chr3 198022430 614072 0.003101022444780624 1.0088175081000215 chr4 191154276 639132 0.0033435401675241624 1.3315082271468905 chr5 180915260 492892 0.0027244357385883314 1.3910388707185515 chr6 171115067 1087738 0.006356763428669902 3.463588801213879 chr7 159138663 1546096 0.009715401467209762 3.844823261920061 chr8 146364022 840708 0.005743952567797023 2.001119150934398 chr9 141213431 687681 0.004869798822464699 2.084661051958858 chr10 135534747 860721 0.006350555994323728 2.572930638518068 chr11 135006516 1141369 0.0084541771302357 2.5652136597665014 chr12 133851895 1173119 0.00876430625057643 2.734538326477068 chr13 115169878 1226049 0.010645570016146062 3.27116477081295 chr14 107349540 284149 0.0026469512584776796 1.0328087195364375 chr15 102531392 754941 0.007363023024207064 2.3520158620299614 chr16 90354753 392395 0.004342826325915583 1.757832606942232 chr17 81195210 874614 0.01077174380114295 3.585725352424373 chr18 78077248 85035 0.001089113694171188 0.3491841747771603 chr19 59128983 289480 0.004895737848222419 1.1713215329336708 chr20 63025520 304988 0.004839119137771493 1.6027009695827688 chr21 48129895 508019 0.010555165349934796 3.9710810089884507 chr22 51304566 96853 0.0018878046838949967 0.5779873216886003 chrMT 16571 934478 56.392372216522844 260.7190278420091 chrX 155270560 30624073 0.19723038932815082 15.687939372116203 chrY 59373566 514565 0.00866656720601892 2.4205228494674604