BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818909.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 = 2,238,202 number of mapped reads = 2,209,189 (98.7%) number of supplementary alignments = 35,441 (1.58%) number of secondary alignments = 0 number of mapped bases = 204,410,199 bp number of sequenced bases = 204,273,078 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 579,325 duplication rate = 22.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1018 >>>>>>> ACTG content number of A's = 58,429,891 bp (28.6%) number of C's = 44,286,855 bp (21.68%) number of T's = 57,608,120 bp (28.2%) number of G's = 43,945,206 bp (21.51%) number of N's = 3,006 bp (0%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,276,336 number of insertions = 31,517 mapped reads with insertion percentage = 1.38% number of deletions = 70,104 mapped reads with deletion percentage = 3.1% homopolymer indels = 40.62% >>>>>>> Coverage mean coverageData = 0.066X std coverageData = 0.8175X There is a 4.28% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 19129627 0.07674856304570651 1.2196204625685143 chr2 243199373 16226796 0.0667221950444749 1.307802193386425 chr3 198022430 12231203 0.06176675541250554 0.35277756957027684 chr4 191154276 8152776 0.04265024131607707 0.4415520692374527 chr5 180915260 10918704 0.06035258717258014 0.38508715540857014 chr6 171115067 9911293 0.057921801824733526 0.3873733052963649 chr7 159138663 17901225 0.11248822041441935 1.7548574641721977 chr8 146364022 18943192 0.12942519439647537 0.6555458163609469 chr9 141213431 7353010 0.0520701887060587 0.6000450615004811 chr10 135534747 7660345 0.056519417858211664 1.0045902951151495 chr11 135006516 8907254 0.0659764747947425 0.45937867094308615 chr12 133851895 7888028 0.05893101476075479 0.3449054932203819 chr13 115169878 6425857 0.05579459761171233 0.3307107277433363 chr14 107349540 6785289 0.06320743433087836 0.40094861983860036 chr15 102531392 5606493 0.054680745970951024 0.3294767579832383 chr16 90354753 5079875 0.05622144747603925 0.9700425041685005 chr17 81195210 5450452 0.0671277529795169 0.469536918105499 chr18 78077248 3539978 0.045339431020929424 0.7274346114767593 chr19 59128983 4001783 0.0676788741656524 0.9800898706004795 chr20 63025520 8433943 0.13381790423942555 0.5730259721399452 chr21 48129895 2008742 0.04173584837448741 0.3552338307713856 chr22 51304566 2464399 0.04803469149315092 0.35001668372463624 chrMT 16571 402182 24.27023112666707 14.11642498206277 chrX 155270560 8221090 0.05294686900079448 0.42299248789399285 chrY 59373566 766663 0.012912530805375577 1.0476712808598267