BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063562.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 = 2,697,506 number of mapped reads = 2,454,272 (90.98%) number of supplementary alignments = 19,735 (0.73%) number of secondary alignments = 0 number of mapped bases = 162,288,783 bp number of sequenced bases = 162,218,708 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,415 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5354 >>>>>>> ACTG content number of A's = 45,459,575 bp (28.02%) number of C's = 29,946,274 bp (18.46%) number of T's = 51,199,545 bp (31.56%) number of G's = 35,609,769 bp (21.95%) number of N's = 3,545 bp (0%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,254,946 number of insertions = 12,219 mapped reads with insertion percentage = 0.49% number of deletions = 42,836 mapped reads with deletion percentage = 1.73% homopolymer indels = 46.33% >>>>>>> Coverage mean coverageData = 0.0524X std coverageData = 0.4669X There is a 4.33% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 17013604 0.06825902351513098 0.8729521369681887 chr2 243199373 11788824 0.04847390786653056 0.54005383195478 chr3 198022430 10355449 0.052294323425886656 0.26844841711483763 chr4 191154276 7076238 0.03701846565022694 0.23823652369391998 chr5 180915260 5748831 0.03177637419861652 0.2103898216764312 chr6 171115067 13122148 0.07668610502896277 0.4064790516287555 chr7 159138663 13591325 0.08540554975003152 0.720454578807073 chr8 146364022 6830170 0.046665634810172135 0.6462002159658095 chr9 141213431 6398625 0.04531173100666324 0.41911458215012914 chr10 135534747 9739385 0.07185895289272204 0.46173445152279713 chr11 135006516 7477317 0.055384860090752955 0.39171973421109435 chr12 133851895 7110022 0.05311857557190356 0.27903375444462153 chr13 115169878 3052193 0.026501660442846003 0.1891255647300654 chr14 107349540 3665340 0.034143974906646085 0.2639875410065504 chr15 102531392 3173077 0.03094737073305315 0.20849341627829235 chr16 90354753 3711429 0.041076189981948154 0.26777555540933434 chr17 81195210 4370779 0.05383050305553739 0.2906014571345431 chr18 78077248 4277142 0.054780901089136746 0.6748464531662103 chr19 59128983 3737343 0.06320661730305763 0.584381369818308 chr20 63025520 2288044 0.036303452950487355 0.23139192188283786 chr21 48129895 2789645 0.05796075391396553 0.3017287273681244 chr22 51304566 1444331 0.02815209468880411 0.1922618608408597 chrMT 16571 81421 4.913463279222738 3.493912840732541 chrX 155270560 12981129 0.08360328577419956 0.40471134974199424 chrY 59373566 464972 0.007831296506596893 0.18753289417704136