BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008663.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 = 1,806,472 number of mapped reads = 1,445,491 (80.02%) number of supplementary alignments = 7,733 (0.43%) number of secondary alignments = 0 number of mapped bases = 93,796,713 bp number of sequenced bases = 93,752,418 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 232,042 duplication rate = 11.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1178 >>>>>>> ACTG content number of A's = 24,494,743 bp (26.13%) number of C's = 17,837,203 bp (19.03%) number of T's = 29,002,813 bp (30.94%) number of G's = 22,356,456 bp (23.85%) number of N's = 61,203 bp (0.07%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 760,529 number of insertions = 6,464 mapped reads with insertion percentage = 0.44% number of deletions = 24,504 mapped reads with deletion percentage = 1.67% homopolymer indels = 48.61% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.3425X There is a 1.52% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 7192853 0.028857914059118833 0.44988247966912137 chr2 243199373 10131253 0.04165822006457229 0.3968745089310291 chr3 198022430 6214641 0.03138352054360711 0.30899666360560196 chr4 191154276 5018001 0.026251052840690837 0.2885604468457857 chr5 180915260 4131840 0.022838537777299713 0.2584226526410291 chr6 171115067 5106868 0.02984464249428135 0.30651167510250393 chr7 159138663 5345019 0.0335871805081082 0.39458655378829705 chr8 146364022 5392805 0.036845154473822805 0.35294244718350687 chr9 141213431 3213986 0.022759775591034256 0.3039092392518192 chr10 135534747 4256303 0.03140377721736552 0.3538770563671433 chr11 135006516 3851395 0.02852747492572877 0.3462863809917689 chr12 133851895 5280925 0.03945349447611481 0.3545426155195451 chr13 115169878 1566870 0.013604859423398886 0.19708685996190473 chr14 107349540 2918896 0.027190577621478397 0.29445808067801127 chr15 102531392 3181575 0.031030252666422398 0.32246118842384625 chr16 90354753 3282362 0.036327496794772936 0.3501554552619249 chr17 81195210 3215515 0.03960227456767462 0.3588981196729841 chr18 78077248 1724826 0.02209127555315474 0.45875411543247 chr19 59128983 2694916 0.04557690430765569 0.4273270730719114 chr20 63025520 2150948 0.03412820711356289 0.33350211655255013 chr21 48129895 1614904 0.03355303393036698 0.33123021896570637 chr22 51304566 1475418 0.028758025162906552 0.28862670912797317 chrMT 16571 69396 4.187797960292077 3.9390561506798014 chrX 155270560 4506410 0.02902295193628464 0.3022527368132973 chrY 59373566 258788 0.004358640004880287 0.11316031997648539