BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714056.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 303,018 number of mapped reads = 231,230 (76.31%) number of supplementary alignments = 6,671 (2.2%) number of secondary alignments = 0 number of mapped bases = 30,242,303 bp number of sequenced bases = 29,496,809 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 191,581 duplication rate = 43.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.5051 >>>>>>> ACTG content number of A's = 8,094,940 bp (27.44%) number of C's = 5,986,148 bp (20.29%) number of T's = 7,733,578 bp (26.22%) number of G's = 7,681,923 bp (26.04%) number of N's = 220 bp (0%) GC percentage = 46.34% >>>>>>> Mismatches and indels general error rate = 0.0483 number of mismatches = 1,322,496 number of insertions = 35,501 mapped reads with insertion percentage = 14.75% number of deletions = 115,685 mapped reads with deletion percentage = 46.34% homopolymer indels = 29.54% >>>>>>> Coverage mean coverageData = 0.0098X std coverageData = 2.5161X There is a 0.04% 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 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% 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% 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 1444640 0.005795933403110759 0.8891374144869185 chr2 243199373 4076900 0.016763612297635323 7.167806230650039 chr3 198022430 1693039 0.00854973348221209 1.3769755747435792 chr4 191154276 1076500 0.005631576873540616 0.9882125317152515 chr5 180915260 1983305 0.01096261863150737 2.053292142771722 chr6 171115067 1238719 0.007239099523597183 1.0645921422931885 chr7 159138663 1356490 0.00852394995928802 1.1648992669737301 chr8 146364022 2149108 0.014683307896526648 3.202438673702976 chr9 141213431 904337 0.006404043819316308 1.0234736093263168 chr10 135534747 1692979 0.012491106800826508 1.7011447392368362 chr11 135006516 1632253 0.012090179410303426 2.0566513940397306 chr12 133851895 1241111 0.0092722706690107 1.5609505457479171 chr13 115169878 1114661 0.009678407404408295 1.588228820444872 chr14 107349540 1186308 0.0110508903904013 2.3077467428672023 chr15 102531392 825298 0.00804922262247254 1.1124478639982318 chr16 90354753 639441 0.0070770045710821655 0.8988038229708922 chr17 81195210 672978 0.008288395337606738 2.0001461745025324 chr18 78077248 866152 0.011093526247236583 1.5261462272769892 chr19 59128983 443460 0.007499875314953413 1.1007587404850898 chr20 63025520 575279 0.009127715249314881 1.265853601249336 chr21 48129895 285213 0.005925901147301485 1.0373911965767042 chr22 51304566 185991 0.0036252328886282755 0.6047169806373612 chrMT 16571 109871 6.630318025466176 51.43930777002115 chrX 155270560 2759659 0.01777322758416019 1.5467221898512196 chrY 59373566 88611 0.001492431834058948 0.29345645000203197