BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819107.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,003,948 number of mapped reads = 1,832,291 (91.43%) number of supplementary alignments = 6,433 (0.32%) number of secondary alignments = 0 number of mapped bases = 106,763,266 bp number of sequenced bases = 106,730,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,490 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0215 >>>>>>> ACTG content number of A's = 27,122,887 bp (25.41%) number of C's = 20,097,670 bp (18.83%) number of T's = 32,378,877 bp (30.34%) number of G's = 27,129,612 bp (25.42%) number of N's = 1,546 bp (0%) GC percentage = 44.25% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 539,868 number of insertions = 6,142 mapped reads with insertion percentage = 0.33% number of deletions = 19,826 mapped reads with deletion percentage = 1.07% homopolymer indels = 44.02% >>>>>>> Coverage mean coverageData = 0.0345X std coverageData = 0.3132X There is a 3.03% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% 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% 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 10579157 0.04244385413186192 0.6002471866134377 chr2 243199373 8453862 0.03476103534197845 0.36628983649885266 chr3 198022430 5824657 0.029414127480407143 0.19128623360272687 chr4 191154276 5991593 0.031344279214554426 0.2251925870054044 chr5 180915260 5858072 0.032380198331528255 0.20022470039211862 chr6 171115067 4574271 0.02673213458169642 0.23431700296384322 chr7 159138663 5280846 0.033183928408396894 0.36873037604796155 chr8 146364022 9758268 0.06667122060911937 0.34177190141188485 chr9 141213431 4497254 0.03184721147381512 0.2578020303211547 chr10 135534747 5503727 0.04060749823807175 0.31981531820166104 chr11 135006516 3696413 0.02737951551908798 0.2986657252410646 chr12 133851895 4931398 0.03684219786354164 0.21481733074550277 chr13 115169878 2350280 0.02040707206445074 0.15888626065764677 chr14 107349540 2548630 0.023741415193767948 0.17649944229845235 chr15 102531392 2834304 0.027643280216072753 0.19060291294527504 chr16 90354753 3368694 0.037282975030655 0.23060965308758452 chr17 81195210 3833538 0.0472138442649511 0.2573956401064868 chr18 78077248 2487959 0.03186535211896813 0.47157988497371034 chr19 59128983 2218113 0.037513126177056016 0.41245627209149854 chr20 63025520 3075133 0.04879187034077624 0.24950215153889582 chr21 48129895 1479332 0.030736239919077323 0.2203728831936427 chr22 51304566 917131 0.017876206184065567 0.14886835020030195 chrMT 16571 8748 0.5279102045742562 0.8733682803989515 chrX 155270560 6338574 0.04082276769015324 0.2544896597120593 chrY 59373566 353312 0.0059506616126105685 0.18171780076880256