BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714146.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 = 667,136 number of mapped reads = 623,300 (93.43%) number of supplementary alignments = 25,120 (3.77%) number of secondary alignments = 0 number of mapped bases = 80,609,889 bp number of sequenced bases = 79,224,675 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 556,653 duplication rate = 42.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.7181 >>>>>>> ACTG content number of A's = 23,596,644 bp (29.78%) number of C's = 15,834,141 bp (19.99%) number of T's = 22,196,156 bp (28.02%) number of G's = 17,597,189 bp (22.21%) number of N's = 545 bp (0%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0396 number of mismatches = 2,848,143 number of insertions = 96,721 mapped reads with insertion percentage = 15.11% number of deletions = 250,467 mapped reads with deletion percentage = 38.43% homopolymer indels = 27.13% >>>>>>> Coverage mean coverageData = 0.026X std coverageData = 5.5818X There is a 0.07% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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 5210036 0.02090280047888025 4.093184050853231 chr2 243199373 10747469 0.044192009491735 10.815534443919734 chr3 198022430 4767086 0.024073464809011787 3.9916692162411334 chr4 191154276 4211876 0.022033909406243155 3.618200772456747 chr5 180915260 5728664 0.03166490212047342 5.798863620338656 chr6 171115067 3796633 0.022187601983640635 4.6925493614398 chr7 159138663 2231075 0.014019691745179485 1.9852928835263755 chr8 146364022 4374607 0.029888540504851662 6.883007126997825 chr9 141213431 2787932 0.01974268297468107 4.261526291061407 chr10 135534747 3269616 0.024123821177753038 3.1625903998592224 chr11 135006516 4462681 0.03305530082710971 9.725846190993659 chr12 133851895 2822691 0.02108816614064373 3.5068810029802115 chr13 115169878 2906495 0.025236590074359546 6.066102302470316 chr14 107349540 2533463 0.023600129073678377 3.7472772924104416 chr15 102531392 1883388 0.01836889135378168 4.4607900378489544 chr16 90354753 1850457 0.020479907681226244 4.353114476909192 chr17 81195210 802847 0.009887861611540878 1.723786193779408 chr18 78077248 1993991 0.025538694703993666 5.426657726923161 chr19 59128983 815345 0.0137892613509013 4.6571523099297325 chr20 63025520 835500 0.013256534813199479 1.457626543719905 chr21 48129895 959981 0.019945628387512584 5.218934569603878 chr22 51304566 380312 0.0074128294935776285 1.1736193609411634 chrMT 16571 4020 0.24259248084002172 1.9361779208685657 chrX 155270560 10789075 0.06948564492843975 6.862293904811539 chrY 59373566 444649 0.007489006134480789 2.1402317174750247