BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472838.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,512,633 number of mapped reads = 2,208,075 (87.88%) number of supplementary alignments = 13,213 (0.53%) number of secondary alignments = 0 number of mapped bases = 144,268,731 bp number of sequenced bases = 144,208,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,178 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8492 >>>>>>> ACTG content number of A's = 38,761,667 bp (26.88%) number of C's = 28,351,951 bp (19.66%) number of T's = 43,436,711 bp (30.12%) number of G's = 33,654,994 bp (23.34%) number of N's = 3,658 bp (0%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,211,197 number of insertions = 11,228 mapped reads with insertion percentage = 0.5% number of deletions = 33,567 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.02% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.3334X There is a 4.03% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 10668592 0.04280266968723019 0.43861617203454273 chr2 243199373 14171952 0.058272979182392874 0.47138592580861693 chr3 198022430 10542462 0.0532387265422407 0.25767417885776794 chr4 191154276 8042820 0.0420750200743613 0.25099072705233455 chr5 180915260 7265173 0.04015787833486241 0.22460938340032366 chr6 171115067 8751618 0.051144637076289724 0.2787137830574144 chr7 159138663 8769000 0.055102888479086946 0.4233993749397018 chr8 146364022 8228641 0.05622038044294793 0.3480669792296731 chr9 141213431 8301287 0.05878539272939272 0.3932799593998334 chr10 135534747 6093897 0.044961879775375975 0.2990468125371896 chr11 135006516 4890984 0.036227762517773585 0.322215235427489 chr12 133851895 5200813 0.03885498221747253 0.236654336153394 chr13 115169878 5678646 0.04930669458554085 0.25665033997287073 chr14 107349540 3005138 0.027993953211164203 0.21606144909874744 chr15 102531392 2762385 0.026941846259143736 0.19245966320129645 chr16 90354753 4873597 0.05393846851642658 0.2847480084115909 chr17 81195210 3219005 0.03964525739880468 0.24191887524908734 chr18 78077248 2481623 0.03178420171776546 0.6047741552914573 chr19 59128983 3336144 0.056421467624430476 0.36082302750896994 chr20 63025520 6226804 0.09879813764329116 0.3735981693621386 chr21 48129895 2174576 0.04518139921144644 0.2798095288944148 chr22 51304566 1713042 0.03338965970397255 0.21889609395853943 chrMT 16571 18719 1.1296240420010861 1.3549468233084665 chrX 155270560 7146922 0.046028828645945506 0.2667325100297681 chrY 59373566 704891 0.011872135151862025 0.15440900679388408