BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236116.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,495,984 number of mapped reads = 1,321,459 (88.33%) number of supplementary alignments = 9,879 (0.66%) number of secondary alignments = 0 number of mapped bases = 86,846,548 bp number of sequenced bases = 86,801,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,650 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0235 >>>>>>> ACTG content number of A's = 24,601,459 bp (28.34%) number of C's = 15,981,073 bp (18.41%) number of T's = 27,381,067 bp (31.54%) number of G's = 18,837,133 bp (21.7%) number of N's = 886 bp (0%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 657,424 number of insertions = 6,552 mapped reads with insertion percentage = 0.49% number of deletions = 25,912 mapped reads with deletion percentage = 1.94% homopolymer indels = 46.42% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.2941X There is a 2.47% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8367911 0.03357227743877918 0.4930290357499422 chr2 243199373 7645265 0.03143620357935709 0.3086875657926707 chr3 198022430 7455832 0.03765145190875599 0.21331931246202315 chr4 191154276 4703163 0.024604016705333864 0.18918227637895274 chr5 180915260 4938896 0.027299499224111887 0.1832654183782832 chr6 171115067 5993182 0.03502427988997602 0.2827883095736918 chr7 159138663 4994136 0.03138229205809025 0.33108871236157356 chr8 146364022 6384040 0.04361754967351198 0.630275232994547 chr9 141213431 3471870 0.024585975819821276 0.2532139251001905 chr10 135534747 3896212 0.028746960364341108 0.2605694896838493 chr11 135006516 3556278 0.02634152858222043 0.21487728153572955 chr12 133851895 2591925 0.019364126297950434 0.16076071625283317 chr13 115169878 2186965 0.01898903635202253 0.15015192484710388 chr14 107349540 2660329 0.02478193199523724 0.18415351332465757 chr15 102531392 2230182 0.021751211570403727 0.16619990531567944 chr16 90354753 1969686 0.02179947301720807 0.1751398280381792 chr17 81195210 1972048 0.024287738155982355 0.1822992107659734 chr18 78077248 2495658 0.031963959590379 0.39397817490701537 chr19 59128983 1523787 0.025770559929975456 0.33785157081552 chr20 63025520 1287459 0.020427582350768386 0.16154759095603763 chr21 48129895 1425790 0.029623792031958515 0.19969797836967673 chr22 51304566 954534 0.018605244609222502 0.14877431438294839 chrMT 16571 75312 4.544807193289482 3.28905297007137 chrX 155270560 3862685 0.0248771241631382 0.18851403509079642 chrY 59373566 203403 0.00342581747574333 0.10174623140504012