BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524298.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,573,454 number of mapped reads = 1,438,204 (91.4%) number of supplementary alignments = 6,372 (0.4%) number of secondary alignments = 0 number of mapped bases = 83,758,988 bp number of sequenced bases = 83,736,291 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,028 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.11 >>>>>>> ACTG content number of A's = 20,584,841 bp (24.58%) number of C's = 15,842,738 bp (18.92%) number of T's = 26,780,088 bp (31.98%) number of G's = 20,516,855 bp (24.5%) number of N's = 11,769 bp (0.01%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 424,475 number of insertions = 6,468 mapped reads with insertion percentage = 0.45% number of deletions = 14,302 mapped reads with deletion percentage = 0.99% homopolymer indels = 40.8% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.2608X There is a 2.47% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 7129289 0.028602893631306137 0.4966807614204784 chr2 243199373 5353289 0.022011935861364247 0.3084867575034873 chr3 198022430 5851780 0.029551096812618652 0.18483887987435232 chr4 191154276 4431381 0.02318222271941225 0.1804245498224147 chr5 180915260 4923765 0.02721586338266877 0.17786054199743298 chr6 171115067 5314435 0.03105766834664536 0.20226032523429463 chr7 159138663 3835796 0.024103482633883885 0.32225150538042474 chr8 146364022 8770084 0.0599196706961223 0.3291148053120912 chr9 141213431 3488122 0.024701064022727412 0.2041499802842679 chr10 135534747 4283626 0.03160537127796461 0.2656169280943098 chr11 135006516 4037805 0.029908223096431878 0.2201549172106328 chr12 133851895 3343117 0.024976239596757297 0.172445878346631 chr13 115169878 2123844 0.01844096769816844 0.14479977540836822 chr14 107349540 1760801 0.01640250158500912 0.14828798929908732 chr15 102531392 2560608 0.024973892873706424 0.17093150004560811 chr16 90354753 2627178 0.029076256785296066 0.19192996917568358 chr17 81195210 2372045 0.029214100191378285 0.19978268496609364 chr18 78077248 1956411 0.025057376509991746 0.34376348143876667 chr19 59128983 1484124 0.025099772137126053 0.331474388655008 chr20 63025520 1891187 0.030006686180455155 0.18809729577936538 chr21 48129895 1211420 0.025169803507778275 0.18182382354110116 chr22 51304566 617327 0.012032593746139476 0.11640027861360963 chrMT 16571 76574 4.620964335284533 3.243559997397732 chrX 155270560 4071224 0.026220192675288863 0.19001239534992248 chrY 59373566 243756 0.004105463363948866 0.12674379658926935