BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230373.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 = 1,908,656 number of mapped reads = 1,467,334 (76.88%) number of supplementary alignments = 16,055 (0.84%) number of secondary alignments = 0 number of mapped bases = 96,479,722 bp number of sequenced bases = 96,437,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 297,607 duplication rate = 13.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1607 >>>>>>> ACTG content number of A's = 27,210,868 bp (28.22%) number of C's = 17,619,678 bp (18.27%) number of T's = 30,836,151 bp (31.98%) number of G's = 20,729,850 bp (21.5%) number of N's = 40,654 bp (0.04%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 829,502 number of insertions = 7,718 mapped reads with insertion percentage = 0.52% number of deletions = 25,848 mapped reads with deletion percentage = 1.74% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 0.4976X There is a 1.05% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 7218184 0.028959542692573673 0.6909396071993242 chr2 243199373 6974182 0.02867680912976696 0.5007305498996486 chr3 198022430 6689384 0.033780940876243164 0.46773839350512875 chr4 191154276 7108063 0.037184954209447035 0.491252375002427 chr5 180915260 6737604 0.03724176722295289 0.4778630475944018 chr6 171115067 8274193 0.048354555475819086 0.596626440073314 chr7 159138663 3507683 0.02204167694936585 0.41688865349040677 chr8 146364022 6937029 0.04739572543312591 0.6415801521924865 chr9 141213431 4775584 0.033818199630033775 0.4924785961619551 chr10 135534747 3246915 0.023956329073311362 0.420025703288492 chr11 135006516 4426822 0.03278969142496796 0.5084566545343425 chr12 133851895 4172233 0.031170518728927968 0.4355187138010174 chr13 115169878 2051940 0.01781663778440401 0.34555095808934977 chr14 107349540 3227297 0.0300634450785723 0.46247852272200435 chr15 102531392 3298895 0.03217448759497969 0.5080156511847903 chr16 90354753 2770837 0.03066620081402912 0.4208607958493597 chr17 81195210 2598352 0.032001296628212425 0.42497481799215103 chr18 78077248 2907705 0.03724138688904609 0.6263097848922371 chr19 59128983 1907534 0.03226055824433848 0.498691628281523 chr20 63025520 1456753 0.023113700608896205 0.38577083124647954 chr21 48129895 895317 0.018602097511328457 0.3362716068977975 chr22 51304566 982427 0.019148919415866415 0.32624856223063525 chrMT 16571 12329 0.7440106209643352 1.6735597353562999 chrX 155270560 4027101 0.025936024189002732 0.4171389623618383 chrY 59373566 275359 0.004637737271835753 0.16462778910419223