BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549025.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 = 8,714,080 number of mapped reads = 7,669,292 (88.01%) number of secondary alignments = 0 number of mapped bases = 303,740,859 bp number of sequenced bases = 303,710,027 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 311,686 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.185 >>>>>>> ACTG content number of A's = 87,397,877 bp (28.78%) number of C's = 63,881,254 bp (21.03%) number of T's = 87,848,272 bp (28.93%) number of G's = 64,579,494 bp (21.26%) number of N's = 3,130 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 824,622 number of insertions = 9,246 mapped reads with insertion percentage = 0.12% number of deletions = 23,677 mapped reads with deletion percentage = 0.31% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.0981X std coverageData = 0.8112X There is a 7.48% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.12% 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% 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 24072226 0.0965783992971476 0.7908435951347402 chr2 243199373 25548716 0.1050525570228341 0.5535307142323387 chr3 198022430 20658210 0.10432257598293285 0.40349315001132663 chr4 191154276 19224654 0.10057140442937305 0.40509067740020804 chr5 180915260 18793238 0.10387867778538969 0.4048573947710669 chr6 171115067 17771574 0.10385744698916548 0.42779390491373726 chr7 159138663 16825417 0.10572802788974041 0.7987591667903423 chr8 146364022 15566877 0.1063572644922261 2.8403523896588223 chr9 141213431 12834500 0.09088724712028277 0.5448364845600422 chr10 135534747 14139879 0.10432659751819952 0.47429568296811964 chr11 135006516 13876976 0.10278745360705405 0.6555120037425899 chr12 133851895 13828036 0.10330848136292729 0.41202554129958696 chr13 115169878 9859531 0.08560859116304699 0.3646394763461816 chr14 107349540 9368522 0.08727118905213753 0.42702095401897655 chr15 102531392 8851260 0.08632731719861952 0.3660181370541021 chr16 90354753 8571293 0.09486266870764397 0.42112349698836304 chr17 81195210 8276301 0.10193090208153904 0.43866302745476726 chr18 78077248 7994532 0.10239259457505469 0.9307289478530704 chr19 59128983 6097542 0.1031227274786715 0.7708517851170148 chr20 63025520 6348955 0.10073625731291071 0.40850178013738053 chr21 48129895 3776852 0.07847205982892753 0.3838384654798756 chr22 51304566 3502735 0.06827335796973705 0.361362250714536 chrMT 16571 32343 1.951783235773339 2.4959950481193682 chrX 155270560 17059144 0.10986721500843431 0.4871626776967912 chrY 59373566 861546 0.014510598874926933 0.1732610361527858