BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231815.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 = 4,559,953 number of mapped reads = 4,188,698 (91.86%) number of supplementary alignments = 35,698 (0.78%) number of secondary alignments = 0 number of mapped bases = 271,336,258 bp number of sequenced bases = 271,230,461 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 462,388 duplication rate = 9.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2945 >>>>>>> ACTG content number of A's = 72,923,568 bp (26.89%) number of C's = 48,852,422 bp (18.01%) number of T's = 87,820,825 bp (32.38%) number of G's = 61,526,583 bp (22.68%) number of N's = 107,063 bp (0.04%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,687,234 number of insertions = 18,204 mapped reads with insertion percentage = 0.43% number of deletions = 61,001 mapped reads with deletion percentage = 1.44% homopolymer indels = 45.01% >>>>>>> Coverage mean coverageData = 0.0876X std coverageData = 0.8891X There is a 6.55% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 26476465 0.1062242689457532 1.8063313857391567 chr2 243199373 18870832 0.07759408162618905 1.1596277792281318 chr3 198022430 20458370 0.10331339737624672 0.4093559652648926 chr4 191154276 11590059 0.06063196305375874 0.3620245957779533 chr5 180915260 18485605 0.10217825185117055 0.41390911216130083 chr6 171115067 16587066 0.09693515767375412 0.6027067120872668 chr7 159138663 19824773 0.12457546536004264 1.5182546268731445 chr8 146364022 17250281 0.11785875220072867 1.3515966068944318 chr9 141213431 9560447 0.06770210830724735 0.5290489032366908 chr10 135534747 14645290 0.10805561174655824 0.6355069082088093 chr11 135006516 13570423 0.10051680024096023 0.6750444877725874 chr12 133851895 9689194 0.07238742492214996 0.3545175978859806 chr13 115169878 9813196 0.08520627242480885 0.4024416656055826 chr14 107349540 12330617 0.11486418106682153 0.4719381979168302 chr15 102531392 5540765 0.05403969352137539 0.33464796326164387 chr16 90354753 7227897 0.07999465174787208 0.42593566328444976 chr17 81195210 6777234 0.08346839671946166 0.4449412361373209 chr18 78077248 5183294 0.06638674047527905 1.315161443065562 chr19 59128983 7106201 0.12018134998195386 1.11368266848303 chr20 63025520 5018925 0.07963321841692064 0.4035449532175556 chr21 48129895 4797492 0.09967800677728468 0.42312369954409335 chr22 51304566 2354383 0.045890320951160565 0.26345018916832746 chrMT 16571 292997 17.681310723553196 10.634564248158936 chrX 155270560 7309153 0.04707365646134077 0.35903716298035343 chrY 59373566 575299 0.009689480332038671 0.20697462905209013