BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472803.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,985,399 number of mapped reads = 2,300,973 (77.07%) number of supplementary alignments = 19,966 (0.67%) number of secondary alignments = 0 number of mapped bases = 146,067,913 bp number of sequenced bases = 146,002,551 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,593 duplication rate = 3.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1978 >>>>>>> ACTG content number of A's = 39,262,315 bp (26.89%) number of C's = 28,956,117 bp (19.83%) number of T's = 43,251,853 bp (29.62%) number of G's = 34,528,811 bp (23.65%) number of N's = 3,455 bp (0%) GC percentage = 43.48% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,322,295 number of insertions = 11,475 mapped reads with insertion percentage = 0.49% number of deletions = 35,992 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0472X std coverageData = 0.3623X There is a 3.77% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% 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% 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 11840222 0.047503279841377005 0.4396026755151094 chr2 243199373 12827114 0.052743203412781825 0.48118177850454236 chr3 198022430 10550639 0.05328001984421664 0.28500592190140756 chr4 191154276 7037507 0.036815849204440504 0.26144573813906136 chr5 180915260 8114265 0.04485119165735384 0.26549700051701863 chr6 171115067 9723239 0.05682281034901503 0.3234898734045412 chr7 159138663 8147170 0.05119541566086929 0.4965097018597222 chr8 146364022 7544099 0.05154339773472472 0.34964214344024763 chr9 141213431 6961148 0.04929522603271356 0.39772580356932663 chr10 135534747 6986521 0.051547821902821714 0.34814457451149067 chr11 135006516 5652676 0.04186965316548129 0.39336117586989017 chr12 133851895 6955249 0.05196227516988086 0.29195397954386365 chr13 115169878 6038189 0.05242854385935878 0.2908593320023268 chr14 107349540 3823674 0.03561891369073403 0.28021846856166244 chr15 102531392 3520658 0.03433736664767021 0.2529721492958782 chr16 90354753 4457677 0.04933527957295174 0.3048259203815578 chr17 81195210 3710995 0.045704604988397714 0.2900366652304494 chr18 78077248 3121373 0.03997800998313875 0.6531877152522341 chr19 59128983 3307382 0.055935039505076556 0.37669594654974004 chr20 63025520 4419342 0.07011988159716889 0.3431517641865587 chr21 48129895 2046837 0.042527352282817156 0.2905805850090565 chr22 51304566 1943205 0.03787586859228085 0.2510094437435004 chrMT 16571 143401 8.653732424114416 6.22515976136509 chrX 155270560 6520237 0.04199274479334653 0.29873405507496853 chrY 59373566 675094 0.011370278820712908 0.16419420756209635