BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094112.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 = 307,974 number of mapped reads = 291,068 (94.51%) number of supplementary alignments = 20,396 (6.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 146,147 number of mapped paired reads (second in pair) = 144,921 number of mapped paired reads (both in pair) = 288,988 number of mapped paired reads (singletons) = 2,080 number of mapped bases = 35,512,514 bp number of sequenced bases = 34,853,392 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 276,490 duplication rate = 52.36% >>>>>>> Insert size mean insert size = 1,665,398.3601 std insert size = 11,529,664.9716 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 40.1417 >>>>>>> ACTG content number of A's = 9,867,626 bp (28.31%) number of C's = 7,651,898 bp (21.95%) number of T's = 9,369,470 bp (26.88%) number of G's = 7,964,040 bp (22.85%) number of N's = 358 bp (0%) GC percentage = 44.8% >>>>>>> Mismatches and indels general error rate = 0.0343 number of mismatches = 1,151,229 number of insertions = 22,366 mapped reads with insertion percentage = 7.6% number of deletions = 93,804 mapped reads with deletion percentage = 31.27% homopolymer indels = 28.54% >>>>>>> Coverage mean coverageData = 0.0115X std coverageData = 2.7981X There is a 0.02% 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 0.01% 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% 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 640335 0.002569040740724975 1.026315889523019 chr2 243199373 2189516 0.009002967289722412 3.7650270228341545 chr3 198022430 589426 0.002976561796560117 0.818487133445617 chr4 191154276 1569405 0.008210148539915476 2.428283581354014 chr5 180915260 658997 0.003642572771362681 1.2739800458781976 chr6 171115067 923197 0.005395182412545822 1.8684823390963103 chr7 159138663 1084949 0.0068176329972057135 2.206323918057667 chr8 146364022 841044 0.005746248213922407 1.8590174483385098 chr9 141213431 609701 0.004317585060304922 1.53017314778988 chr10 135534747 335817 0.002477718868652922 0.6596358392307906 chr11 135006516 1384722 0.010256704943041416 3.3533986522868307 chr12 133851895 701353 0.005239768925199005 1.164235364452077 chr13 115169878 912547 0.007923486729750639 2.4828539393926303 chr14 107349540 98355 9.162125892668007E-4 0.27923611206709487 chr15 102531392 491666 0.004795272846778478 1.365287904131333 chr16 90354753 92774 0.0010267749832706642 0.38073033242375054 chr17 81195210 375952 0.004630223876507001 1.5457644761076783 chr18 78077248 183681 0.002352554741683518 0.6307054739595088 chr19 59128983 72666 0.0012289404673170177 0.4193736076899337 chr20 63025520 179806 0.0028529078379678583 0.8763437995170257 chr21 48129895 186538 0.0038757200696157763 1.5135957583798987 chr22 51304566 33835 6.594929581901151E-4 0.18508022807154192 chrMT 16571 26355 1.5904290628205902 7.890394380383574 chrX 155270560 20823205 0.13410916402954945 9.328053441575676 chrY 59373566 506672 0.00853362925851548 1.7128430128218213