BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238325.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 = 2,854,301 number of mapped reads = 2,008,044 (70.35%) number of supplementary alignments = 26,237 (0.92%) number of secondary alignments = 0 number of mapped bases = 130,281,461 bp number of sequenced bases = 130,223,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,754 duplication rate = 6.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9305 >>>>>>> ACTG content number of A's = 36,750,538 bp (28.22%) number of C's = 25,025,539 bp (19.22%) number of T's = 40,175,643 bp (30.85%) number of G's = 28,231,814 bp (21.68%) number of N's = 39,823 bp (0.03%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,131,744 number of insertions = 9,437 mapped reads with insertion percentage = 0.47% number of deletions = 34,371 mapped reads with deletion percentage = 1.69% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.0421X std coverageData = 0.4702X There is a 2.97% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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% 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 13648835 0.05475948242471981 1.062768010047874 chr2 243199373 13932954 0.0572902546093324 0.5359919861428575 chr3 198022430 10279476 0.05191066486761121 0.30669228304491153 chr4 191154276 11103898 0.05808867179094649 0.3328340242456678 chr5 180915260 6853951 0.03788486941344804 0.26357483332749826 chr6 171115067 6670570 0.0389829494091248 0.3047211951613146 chr7 159138663 6700650 0.04210573265907104 0.5667412106991977 chr8 146364022 6268301 0.042826788402958754 0.4556402285115616 chr9 141213431 7213155 0.05107980840717623 0.39760167257210377 chr10 135534747 5272965 0.03890489425564059 0.4055098585413384 chr11 135006516 7101413 0.05260052040747426 0.3642409603003757 chr12 133851895 6457764 0.04824559263804222 0.3033486894551806 chr13 115169878 2488507 0.021607273040612232 0.1985435477809503 chr14 107349540 3689019 0.03436455340190559 0.2756610796248871 chr15 102531392 2168716 0.02115172687794973 0.20123889733771042 chr16 90354753 2878574 0.03185857859630251 0.2649519683817034 chr17 81195210 2080117 0.02561871568532183 0.22054084199968996 chr18 78077248 2551692 0.032681633451015074 0.6304896135103816 chr19 59128983 2799222 0.04734094614818591 0.6957809430057118 chr20 63025520 1605751 0.02547779058387777 0.22882587766938145 chr21 48129895 1492428 0.03100833691825008 0.24468260686642 chr22 51304566 834707 0.016269643524515928 0.16567610347509112 chrMT 16571 59009 3.560980025345483 3.2565008616018045 chrX 155270560 5817308 0.037465621300006906 0.2811197032189353 chrY 59373566 312479 0.0052629313186275525 0.1137951601304177