BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231870.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 = 6,319,117 number of mapped reads = 5,476,215 (86.66%) number of supplementary alignments = 42,893 (0.68%) number of secondary alignments = 0 number of mapped bases = 353,093,803 bp number of sequenced bases = 352,959,071 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 839,634 duplication rate = 12.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9726 >>>>>>> ACTG content number of A's = 92,042,295 bp (26.08%) number of C's = 63,745,482 bp (18.06%) number of T's = 114,737,815 bp (32.51%) number of G's = 82,297,185 bp (23.32%) number of N's = 136,294 bp (0.04%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 2,211,865 number of insertions = 24,565 mapped reads with insertion percentage = 0.44% number of deletions = 76,148 mapped reads with deletion percentage = 1.38% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 0.1141X std coverageData = 1.2594X There is a 7.48% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 27343523 0.10970292828277448 3.1201117687366215 chr2 243199373 27080885 0.11135261027173783 1.7896370859852482 chr3 198022430 36031880 0.18195857913671698 0.5963414638754573 chr4 191154276 18712445 0.0978918462697638 0.5428709585569476 chr5 180915260 31942024 0.17655793104462278 0.6281823963184207 chr6 171115067 19914995 0.11638364376177347 0.9242191779758867 chr7 159138663 17883198 0.1123749418455275 1.0847831666492813 chr8 146364022 22641388 0.15469230546288212 1.0118462694273431 chr9 141213431 24700213 0.17491404907511948 1.0412119526758299 chr10 135534747 9800238 0.07230793738818873 0.7030273001895341 chr11 135006516 4922882 0.036464032595285994 0.5752271154665781 chr12 133851895 6055439 0.0452398451288269 0.4289914662661061 chr13 115169878 2981328 0.025886351985195295 0.3053076619150916 chr14 107349540 27250440 0.2538477575218301 0.7883744000995261 chr15 102531392 1061436 0.010352302639176107 0.24945923117550634 chr16 90354753 4826429 0.053416437317912874 0.4742948803928036 chr17 81195210 18929420 0.23313468861032566 0.8799116769550844 chr18 78077248 10779621 0.1380635367680992 2.028534610983309 chr19 59128983 19570222 0.3309751158750692 1.6360042715202658 chr20 63025520 11869436 0.18832745846444424 0.6325269979203136 chr21 48129895 1900020 0.03947691969824576 0.39539274933951646 chr22 51304566 3692215 0.07196659650137183 0.3627930045204446 chrMT 16571 95427 5.75867479331362 4.258854812254219 chrX 155270560 2481167 0.015979635804752684 0.39572257619487095 chrY 59373566 627532 0.010569215263236842 0.3559930579750085