BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004019.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 = 2,126,257 number of mapped reads = 1,864,726 (87.7%) number of supplementary alignments = 14,895 (0.7%) number of secondary alignments = 0 number of mapped bases = 124,611,531 bp number of sequenced bases = 124,560,260 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,366 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0217 >>>>>>> ACTG content number of A's = 34,357,021 bp (27.58%) number of C's = 23,712,205 bp (19.04%) number of T's = 38,741,572 bp (31.1%) number of G's = 27,726,707 bp (22.26%) number of N's = 22,755 bp (0.02%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,083,907 number of insertions = 8,743 mapped reads with insertion percentage = 0.47% number of deletions = 29,390 mapped reads with deletion percentage = 1.56% homopolymer indels = 46.22% >>>>>>> Coverage mean coverageData = 0.0403X std coverageData = 0.3221X There is a 3.33% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11141213 0.04469883748052929 0.5202280566530278 chr2 243199373 9418204 0.038726267604316564 0.37301148136053985 chr3 198022430 8310255 0.041966230795168 0.237260133185937 chr4 191154276 8190830 0.04284931611992818 0.25498657535686176 chr5 180915260 6489590 0.03587088231252576 0.21999861344778657 chr6 171115067 6995935 0.040884389216292685 0.25359543193016937 chr7 159138663 8126380 0.051064774874978056 0.4549308845236738 chr8 146364022 8850179 0.06046690217354098 0.4197058043409712 chr9 141213431 5079147 0.035967874755482715 0.29416680454943456 chr10 135534747 5509687 0.04065147220144219 0.29873236638523254 chr11 135006516 5611224 0.04156261613328352 0.29545694349687274 chr12 133851895 4956098 0.03702673017815698 0.2286104436782535 chr13 115169878 4103838 0.03563291089012007 0.22656163732773948 chr14 107349540 2953252 0.027510616254154418 0.20873120760259511 chr15 102531392 4161001 0.04058270271020996 0.23720321476017966 chr16 90354753 3163982 0.03501732775474468 0.22873440773531376 chr17 81195210 2752663 0.03390179051202651 0.22573571345048724 chr18 78077248 3228105 0.04134501513168087 0.5068394667678777 chr19 59128983 1937649 0.032769868543147444 0.3612737867604682 chr20 63025520 2908821 0.04615306624998889 0.2666844108261721 chr21 48129895 1655870 0.034404188914187325 0.2310605025360068 chr22 51304566 1290299 0.025149788812169272 0.18317667769168836 chrMT 16571 63825 3.8516082312473596 3.3414545941885567 chrX 155270560 7413722 0.04774711960850789 0.27385879246889505 chrY 59373566 299762 0.005048745093060437 0.10897367303829941