BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234131.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 = 1,327,598 number of mapped reads = 1,019,563 (76.8%) number of supplementary alignments = 1,662 (0.13%) number of secondary alignments = 0 number of mapped bases = 72,690,796 bp number of sequenced bases = 72,686,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 792,935 duplication rate = 6.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.5634 >>>>>>> ACTG content number of A's = 3,378,742 bp (4.65%) number of C's = 2,293,718 bp (3.16%) number of T's = 4,865,607 bp (6.69%) number of G's = 62,141,044 bp (85.49%) number of N's = 7,156 bp (0.01%) GC percentage = 88.65% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 276,214 number of insertions = 2,343 mapped reads with insertion percentage = 0.22% number of deletions = 3,079 mapped reads with deletion percentage = 0.3% homopolymer indels = 37.81% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 118.521X There is a 0.38% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 573578 0.0023012099135351805 0.06973722713514138 chr2 243199373 59520283 0.24473863672337676 422.8562990409321 chr3 198022430 614069 0.0031010072949816847 0.06803256836189724 chr4 191154276 236016 0.0012346885716540289 0.04372240561326632 chr5 180915260 1553316 0.008585876061532896 0.11048380394024856 chr6 171115067 380659 0.0022245790898121204 0.1367979329964515 chr7 159138663 313783 0.001971758428057172 0.14945531250097116 chr8 146364022 202668 0.001384684550414992 0.050887396274727145 chr9 141213431 361875 0.0025626103511357926 0.06419329099752001 chr10 135534747 1484763 0.010954851304662117 0.13954033344858607 chr11 135006516 1160476 0.00859570363255652 0.3745162688190483 chr12 133851895 1679229 0.012545425673652211 0.16041822866760036 chr13 115169878 586689 0.0050941184464917124 0.0939112346463339 chr14 107349540 988819 0.009211208543604379 0.4168195011343092 chr15 102531392 192363 0.00187613760281339 0.1325607695602087 chr16 90354753 202219 0.002238056032315201 0.06050216667697004 chr17 81195210 621958 0.00766003314727556 0.11243085771795122 chr18 78077248 99429 0.0012734695772064098 0.05142821160630811 chr19 59128983 243093 0.00411123255747524 0.08779001462914557 chr20 63025520 234021 0.003713114941376128 0.0726420953532205 chr21 48129895 575236 0.011951740181440245 0.1331637090935437 chr22 51304566 67198 0.0013097859555034536 0.0401497378551395 chrMT 16571 13373 0.8070122503168186 2.5311881813506436 chrX 155270560 739275 0.0047612052149486675 0.08720719756907785 chrY 59373566 46408 7.816272985860408E-4 0.042016995634181147