BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819016.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 = 2,936,914 number of mapped reads = 2,707,615 (92.19%) number of supplementary alignments = 37,016 (1.26%) number of secondary alignments = 0 number of mapped bases = 250,878,014 bp number of sequenced bases = 250,728,245 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,307,637 duplication rate = 37.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3002 >>>>>>> ACTG content number of A's = 71,937,314 bp (28.69%) number of C's = 53,174,387 bp (21.21%) number of T's = 71,771,481 bp (28.63%) number of G's = 53,833,054 bp (21.47%) number of N's = 12,009 bp (0%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,538,326 number of insertions = 41,384 mapped reads with insertion percentage = 1.48% number of deletions = 79,777 mapped reads with deletion percentage = 2.88% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.081X std coverageData = 0.9565X There is a 3.46% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% 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 24882062 0.09982748247596142 1.6176773293024413 chr2 243199373 20417625 0.08395426660906728 1.430964227379557 chr3 198022430 15117512 0.07634242242154084 0.5589387798925521 chr4 191154276 14029626 0.07339425668929321 0.6508819889249445 chr5 180915260 13649165 0.07544507301374136 0.5894802079702749 chr6 171115067 10164879 0.05940376366740399 0.5981427630365161 chr7 159138663 12552232 0.07887606797350057 1.1967359434726692 chr8 146364022 22494551 0.1536890739446884 0.9066683060591728 chr9 141213431 10742141 0.07607025000334423 0.8900460308736676 chr10 135534747 12680226 0.09355701235787159 1.132700440806856 chr11 135006516 8550814 0.0633363059305967 0.6130340042779758 chr12 133851895 11745087 0.08774688621330315 0.6170857354184464 chr13 115169878 5374161 0.04666290434031718 0.4385657394111931 chr14 107349540 5727251 0.053351425632564425 0.513112359552023 chr15 102531392 6469497 0.06309771937944625 0.5158783916971031 chr16 90354753 7814701 0.08648909703731911 1.0960413352911091 chr17 81195210 8718710 0.10737961020114364 0.7831883222559136 chr18 78077248 5908332 0.0756729028154271 1.0588056288755463 chr19 59128983 5071034 0.08576223947568995 1.5029133602560198 chr20 63025520 7171540 0.11378787513375534 0.7408489511972636 chr21 48129895 3601375 0.07482615534482259 0.6273899053628006 chr22 51304566 2053035 0.0400166137259596 0.4475605761310584 chrMT 16571 167337 10.098183573713113 9.671779243447531 chrX 155270560 14838389 0.09556472907678056 0.7595362663533795 chrY 59373566 936732 0.015776919984896984 1.0362027262791924