BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818855.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,673,968 number of mapped reads = 1,630,498 (97.4%) number of supplementary alignments = 25,333 (1.51%) number of secondary alignments = 0 number of mapped bases = 150,937,302 bp number of sequenced bases = 150,840,074 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 365,416 duplication rate = 18.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3443 >>>>>>> ACTG content number of A's = 42,816,544 bp (28.39%) number of C's = 30,959,461 bp (20.52%) number of T's = 44,030,994 bp (29.19%) number of G's = 33,030,739 bp (21.9%) number of N's = 2,336 bp (0%) GC percentage = 42.42% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 943,794 number of insertions = 22,483 mapped reads with insertion percentage = 1.34% number of deletions = 48,633 mapped reads with deletion percentage = 2.91% homopolymer indels = 39.93% >>>>>>> Coverage mean coverageData = 0.0488X std coverageData = 0.6004X There is a 3.38% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.1% 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 14310420 0.057413778720334666 0.888713636194479 chr2 243199373 11543033 0.04746325147803732 0.8423450677438796 chr3 198022430 9321676 0.047073839059544924 0.2932572301630626 chr4 191154276 7573427 0.039619448533811503 0.3677084190858863 chr5 180915260 6614402 0.036560774364749554 0.27431423767667334 chr6 171115067 7407772 0.04329117318465007 0.3102388043667163 chr7 159138663 13497232 0.08481428551401114 1.2852314597461008 chr8 146364022 13099930 0.08950239150984796 0.5044871527637902 chr9 141213431 5497379 0.038929576040114766 0.47719796009562226 chr10 135534747 7041957 0.05195683878762101 0.8543284978355723 chr11 135006516 6534342 0.04840019721714765 0.36569805656090004 chr12 133851895 5982420 0.04469432427534926 0.2916099906948322 chr13 115169878 4612198 0.04004691226641744 0.268935630324411 chr14 107349540 4466292 0.04160513403224644 0.2982851873480749 chr15 102531392 4182695 0.04079428669026555 0.27920887299129377 chr16 90354753 3859786 0.04271812906178826 0.6108394930173918 chr17 81195210 3799531 0.046795014139380885 0.3845344077303065 chr18 78077248 2906000 0.03721954954150023 0.5709395833007924 chr19 59128983 2638207 0.04461783149559667 0.803842562443912 chr20 63025520 6298185 0.0999307106073857 0.45936603689675853 chr21 48129895 1423018 0.029566197890105516 0.29238886199609343 chr22 51304566 1372909 0.026759976880030522 0.23839446571784775 chrMT 16571 238077 14.36708707983827 9.569194575882689 chrX 155270560 6121814 0.03942675288863517 0.3158762288829172 chrY 59373566 594600 0.010014557656853556 0.7802546390225193