BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013273.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,433,886 number of mapped reads = 2,128,901 (87.47%) number of supplementary alignments = 29,415 (1.21%) number of secondary alignments = 0 number of mapped bases = 143,139,932 bp number of sequenced bases = 143,079,920 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 352,159 duplication rate = 10.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5405 >>>>>>> ACTG content number of A's = 40,665,695 bp (28.42%) number of C's = 26,615,303 bp (18.6%) number of T's = 45,307,717 bp (31.67%) number of G's = 30,458,814 bp (21.29%) number of N's = 32,391 bp (0.02%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,243,890 number of insertions = 13,094 mapped reads with insertion percentage = 0.61% number of deletions = 33,473 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.6396X There is a 1.78% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 3058036 0.012268920284856582 0.6417499199104445 chr2 243199373 9653547 0.03969396335573612 0.6834357575525732 chr3 198022430 4861626 0.024550885472923445 0.3189977825243428 chr4 191154276 3424018 0.017912327527530695 0.368233933157492 chr5 180915260 4971414 0.02747924083352615 0.34936128357925333 chr6 171115067 11257349 0.06578818100220245 0.603137335809388 chr7 159138663 10484302 0.06588155136128045 0.7891581859964363 chr8 146364022 2487846 0.016997660804921034 0.7648397025153526 chr9 141213431 4741191 0.033574646309670074 0.5450921841045324 chr10 135534747 13421028 0.0990227841720913 0.8176835505593351 chr11 135006516 2445988 0.018117555155634117 0.5893840890237735 chr12 133851895 1857907 0.013880318989880569 0.24234505385941377 chr13 115169878 12957528 0.11250795976357637 0.7048640299826862 chr14 107349540 15568627 0.14502742163590082 0.8130235259669586 chr15 102531392 11988742 0.11692752596200001 0.7169339409872589 chr16 90354753 8048111 0.08907235903793573 0.6958879314552654 chr17 81195210 1484770 0.018286423546413636 0.3577886107784546 chr18 78077248 1548151 0.01982845245775056 1.5315200725300864 chr19 59128983 3137711 0.05306553302295086 0.7892025870424401 chr20 63025520 705791 0.011198495466598292 0.260317501177688 chr21 48129895 4804811 0.09983007442671546 0.7041946451435095 chr22 51304566 492190 0.009593493101569166 0.18079170012896711 chrMT 16571 36671 2.2129624042001086 2.831808507433971 chrX 155270560 8849649 0.05699502210850531 0.5334789498899551 chrY 59373566 852928 0.014365450106197091 0.49289051727490957