BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549108.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,781,019 number of mapped reads = 9,899,857 (84.03%) number of secondary alignments = 0 number of mapped bases = 392,464,732 bp number of sequenced bases = 392,424,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 410,283 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8642 >>>>>>> ACTG content number of A's = 119,046,288 bp (30.34%) number of C's = 77,551,775 bp (19.76%) number of T's = 118,180,036 bp (30.12%) number of G's = 77,645,370 bp (19.79%) number of N's = 1,491 bp (0%) GC percentage = 39.55% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 1,306,926 number of insertions = 11,699 mapped reads with insertion percentage = 0.12% number of deletions = 31,650 mapped reads with deletion percentage = 0.32% homopolymer indels = 43.14% >>>>>>> Coverage mean coverageData = 0.1268X std coverageData = 1.9686X There is a 9.97% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.11% 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 29022348 0.11643841802103273 1.6680719004930018 chr2 243199373 34289269 0.14099242352898664 0.7220159972943948 chr3 198022430 28041967 0.14161005397216872 0.45466572946854594 chr4 191154276 27775360 0.14530336742244782 0.4990810935588378 chr5 180915260 25748628 0.14232424616917336 0.46927404517330945 chr6 171115067 23989102 0.14019280955545546 0.5107555894545334 chr7 159138663 22336318 0.14035758236827717 1.1394161590245524 chr8 146364022 21783787 0.14883293518676333 8.30464910430033 chr9 141213431 16791519 0.1189087955804997 0.709742170710936 chr10 135534747 18567514 0.1369944933751933 0.6958126417085052 chr11 135006516 18329589 0.13576818025583298 0.684187264973882 chr12 133851895 18062336 0.1349426991676136 0.47390591423014294 chr13 115169878 13554189 0.11768866334997767 0.40852554312982786 chr14 107349540 12389591 0.11541354532120025 0.5829316974997031 chr15 102531392 11212112 0.10935296772329005 0.39519251117301696 chr16 90354753 10030347 0.1110107290094634 0.47123788702711156 chr17 81195210 9230723 0.11368556100784763 0.4517725127915038 chr18 78077248 10847124 0.138928103613488 1.4258912492550813 chr19 59128983 6691764 0.11317231686531798 1.4335817491650016 chr20 63025520 7632898 0.121108052738002 0.46096270714019694 chr21 48129895 5224420 0.10854833570694472 0.49210455127122466 chr22 51304566 3783923 0.07375411771342145 0.39121567985383227 chrMT 16571 107447 6.484038380302938 6.8407323723745375 chrX 155270560 13808514 0.08893195207127481 0.48357532802077247 chrY 59373566 3213943 0.05413087366185821 0.4435271322881837