BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524334.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 = 3,309,231 number of mapped reads = 3,044,021 (91.99%) number of supplementary alignments = 14,633 (0.44%) number of secondary alignments = 0 number of mapped bases = 177,883,008 bp number of sequenced bases = 177,836,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,149 duplication rate = 3.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2187 >>>>>>> ACTG content number of A's = 43,282,363 bp (24.34%) number of C's = 34,011,498 bp (19.13%) number of T's = 56,479,401 bp (31.76%) number of G's = 44,036,674 bp (24.76%) number of N's = 26,114 bp (0.01%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 895,629 number of insertions = 11,562 mapped reads with insertion percentage = 0.38% number of deletions = 29,367 mapped reads with deletion percentage = 0.96% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.0575X std coverageData = 0.4726X There is a 4.84% of reference with a coverageData >= 1X There is a 0.63% 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 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15286996 0.06133182713314082 0.9052158120318607 chr2 243199373 11870013 0.04880774507588883 0.6475923028767974 chr3 198022430 12403270 0.06263568223054328 0.29131518124075845 chr4 191154276 9014975 0.04716072896009922 0.29909518928109147 chr5 180915260 10123421 0.05595670039111129 0.2735832852872721 chr6 171115067 11203876 0.06547568368132071 0.33201515093336476 chr7 159138663 8431515 0.05298219075775445 0.6031223026621478 chr8 146364022 18561085 0.126814532330903 0.5872997975559457 chr9 141213431 7165894 0.05074513061013297 0.3461161248423292 chr10 135534747 9281756 0.06848248294586774 0.4641732098296745 chr11 135006516 8590576 0.06363082504847396 0.40133759329852126 chr12 133851895 6727285 0.05025916891202773 0.2642523353496782 chr13 115169878 3978771 0.034546975902848484 0.2153419697095686 chr14 107349540 3943406 0.03673426080819722 0.23793336521021666 chr15 102531392 5441892 0.053075374222950174 0.27071981439819354 chr16 90354753 5722331 0.06333182051861733 0.31696019844007883 chr17 81195210 5597987 0.06894479366455238 0.34659962647495035 chr18 78077248 4157032 0.05324255281128761 0.6967906989480789 chr19 59128983 3136513 0.05304527223138609 0.6200778583755102 chr20 63025520 4256183 0.06753110486038037 0.31204221627537154 chr21 48129895 2546449 0.05290784449041495 0.3021756746552311 chr22 51304566 1215882 0.02369929413300173 0.18015946754689846 chrMT 16571 198484 11.977792529117133 7.171972334103236 chrX 155270560 8501262 0.05475128060335456 0.3081418703810462 chrY 59373566 526154 0.008861755078008958 0.24898624908812564