BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013222.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 = 1,998,340 number of mapped reads = 1,688,439 (84.49%) number of supplementary alignments = 16,128 (0.81%) number of secondary alignments = 0 number of mapped bases = 109,085,159 bp number of sequenced bases = 109,032,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,108 duplication rate = 4.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3166 >>>>>>> ACTG content number of A's = 29,645,144 bp (27.19%) number of C's = 19,423,870 bp (17.81%) number of T's = 35,383,439 bp (32.45%) number of G's = 24,579,009 bp (22.54%) number of N's = 1,322 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 854,187 number of insertions = 7,631 mapped reads with insertion percentage = 0.45% number of deletions = 30,813 mapped reads with deletion percentage = 1.81% homopolymer indels = 44.93% >>>>>>> Coverage mean coverageData = 0.0352X std coverageData = 0.4307X There is a 2.84% of reference with a coverageData >= 1X There is a 0.49% 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 2977243 0.011944776659152235 0.7233722458622046 chr2 243199373 14286536 0.05874413171287247 0.4576808565541877 chr3 198022430 5132045 0.025916483299391894 0.19063934900886456 chr4 191154276 9725956 0.05088013830253005 0.2698360130212834 chr5 180915260 6654252 0.03678104323537992 0.22930666341732245 chr6 171115067 5309029 0.03102607557053991 0.28582764354467366 chr7 159138663 11198308 0.07036824231707917 1.0928340286109062 chr8 146364022 5682006 0.03882105672116608 0.5236302817217687 chr9 141213431 2208803 0.015641592902023604 0.23625315928382926 chr10 135534747 3235177 0.02386972397565327 0.2624357548294996 chr11 135006516 1391892 0.010309813490779956 0.177466762602334 chr12 133851895 3891140 0.02907048869199797 0.20660292216093487 chr13 115169878 5302408 0.04603988553326418 0.2557971699316232 chr14 107349540 5582434 0.05200240261858598 0.29085338038469577 chr15 102531392 3259383 0.0317891226913217 0.21165567893535323 chr16 90354753 4483580 0.049621960673170123 0.2799376311622559 chr17 81195210 2745337 0.03381156351464575 0.24053919336369214 chr18 78077248 1997288 0.02558092211446797 0.5779851096153017 chr19 59128983 2342867 0.03962298827294222 0.4461681808113301 chr20 63025520 624762 0.0099128416552533 0.14149014737296253 chr21 48129895 3876206 0.08053634856257218 0.35443248117210924 chr22 51304566 790312 0.015404320933150473 0.14535513782430093 chrMT 16571 60347 3.641723492848953 2.9766152984779324 chrX 155270560 6092319 0.03923679414822746 0.25140383294435104 chrY 59373566 235529 0.003966900017425263 0.08366731785425237