BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548948.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 4,400,695 number of mapped reads = 3,770,516 (85.68%) number of secondary alignments = 0 number of mapped bases = 149,553,881 bp number of sequenced bases = 149,539,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 132,939 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9874 >>>>>>> ACTG content number of A's = 42,376,133 bp (28.34%) number of C's = 31,870,365 bp (21.31%) number of T's = 43,178,073 bp (28.87%) number of G's = 32,113,908 bp (21.48%) number of N's = 1,320 bp (0%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0022 number of mismatches = 327,668 number of insertions = 3,793 mapped reads with insertion percentage = 0.1% number of deletions = 10,538 mapped reads with deletion percentage = 0.28% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0483X std coverageData = 0.4939X There is a 4.14% of reference with a coverageData >= 1X There is a 0.53% 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 12269468 0.049225426002047955 0.7328512837032413 chr2 243199373 12647519 0.05200473522602379 0.3243857626706877 chr3 198022430 10283051 0.05192871837801405 0.2583559913885121 chr4 191154276 9711457 0.05080428857369636 0.2621869238969326 chr5 180915260 9723749 0.05374753351375666 0.26369106791181235 chr6 171115067 8841271 0.05166857106744434 0.2705443937706128 chr7 159138663 8357584 0.052517621063587795 0.5499800218363253 chr8 146364022 7876825 0.053816674974947055 1.5437776597466528 chr9 141213431 6260132 0.0443309956826982 0.3019768817969317 chr10 135534747 7136182 0.05265204796523507 0.31381898500084626 chr11 135006516 6977958 0.05168608306283528 0.336443282674358 chr12 133851895 6926844 0.051750063008073215 0.26113954663135447 chr13 115169878 4938999 0.042884468454503354 0.2320477349984619 chr14 107349540 4660017 0.04340975285036154 0.2543818463375205 chr15 102531392 4367874 0.04260035794695931 0.2320991578760993 chr16 90354753 4262014 0.04716978198147473 0.2557443673213081 chr17 81195210 4088804 0.0503576996721851 0.2623721423227087 chr18 78077248 4045572 0.051814992249726834 0.5102646225207556 chr19 59128983 2948171 0.04985999843765282 0.5833923292107617 chr20 63025520 3227189 0.051204480343835325 0.2617865698130121 chr21 48129895 1968638 0.04090260325728946 0.2575553103213335 chr22 51304566 1778629 0.03466804494555124 0.2977610223979683 chrMT 16571 9034 0.5451692716190936 0.9859706905099003 chrX 155270560 4826805 0.03108641457852667 0.23753009435253272 chrY 59373566 1420095 0.02391796713035562 0.2918790034356612