BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094147.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 = 419,294 number of mapped reads = 383,327 (91.42%) number of supplementary alignments = 23,796 (5.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 192,487 number of mapped paired reads (second in pair) = 190,840 number of mapped paired reads (both in pair) = 380,158 number of mapped paired reads (singletons) = 3,169 number of mapped bases = 48,062,388 bp number of sequenced bases = 46,931,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 354,911 duplication rate = 48.6% >>>>>>> Insert size mean insert size = 1,298,383.7418 std insert size = 10,279,100.4796 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 46.0239 >>>>>>> ACTG content number of A's = 12,931,881 bp (27.55%) number of C's = 10,482,528 bp (22.34%) number of T's = 12,272,091 bp (26.15%) number of G's = 11,244,725 bp (23.96%) number of N's = 464 bp (0%) GC percentage = 46.3% >>>>>>> Mismatches and indels general error rate = 0.0405 number of mismatches = 1,839,580 number of insertions = 30,794 mapped reads with insertion percentage = 7.91% number of deletions = 148,323 mapped reads with deletion percentage = 37.49% homopolymer indels = 28.51% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 2.5344X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 866610 0.0034768619493228867 1.0832830793519872 chr2 243199373 2184756 0.008983394870841217 2.520643723908045 chr3 198022430 726960 0.0036710992790059188 0.9774612907011373 chr4 191154276 1101231 0.0057609540473999125 1.4661084643503646 chr5 180915260 1081313 0.005976903219772616 1.8497284315750728 chr6 171115067 670689 0.003919520424230089 1.1950443121909475 chr7 159138663 1084056 0.006812021538725633 1.6851377409223176 chr8 146364022 981767 0.0067077071713702975 1.9237990540365406 chr9 141213431 688912 0.0048785161235831735 1.655948970383147 chr10 135534747 678805 0.005008346678804071 1.1325723607523912 chr11 135006516 893768 0.006620184169481123 1.489228836497479 chr12 133851895 1092488 0.00816191657204405 1.8595989259849761 chr13 115169878 920485 0.00799241100177253 1.5195949858258042 chr14 107349540 204482 0.0019048241846215642 0.5668551099985276 chr15 102531392 543210 0.005297987176454212 1.2210448739306226 chr16 90354753 260074 0.00287836545798537 0.8168454053297471 chr17 81195210 729057 0.00897906415908032 1.76779383890428 chr18 78077248 205993 0.0026383230105651266 0.6301427793052126 chr19 59128983 167729 0.0028366630286876405 0.7164533094165303 chr20 63025520 276039 0.004379797263076925 1.3513543719432213 chr21 48129895 271625 0.005643581811263041 1.5160689176405495 chr22 51304566 152908 0.002980397495224889 0.6067849240163667 chrMT 16571 1353222 81.6620602256955 327.9131615721192 chrX 155270560 30919634 0.19913391179886258 8.529157238450631 chrY 59373566 6575 1.1073951663944186E-4 0.04467164619661093