BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926945.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 12,681,706 number of mapped reads = 12,247,358 (96.58%) number of supplementary alignments = 240,848 (1.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,129,564 number of mapped paired reads (second in pair) = 6,117,794 number of mapped paired reads (both in pair) = 12,083,762 number of mapped paired reads (singletons) = 163,596 number of mapped bases = 1,119,367,342 bp number of sequenced bases = 1,118,551,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 728,611 duplication rate = 4.72% >>>>>>> Insert size mean insert size = 205,587.6745 std insert size = 4,553,893.5386 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 53.1079 >>>>>>> ACTG content number of A's = 312,129,195 bp (27.9%) number of C's = 224,974,586 bp (20.11%) number of T's = 318,504,305 bp (28.47%) number of G's = 262,894,931 bp (23.5%) number of N's = 48,246 bp (0%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 10,125,664 number of insertions = 185,218 mapped reads with insertion percentage = 1.48% number of deletions = 546,419 mapped reads with deletion percentage = 4.35% homopolymer indels = 51.76% >>>>>>> Coverage mean coverageData = 0.3616X std coverageData = 1.5886X There is a 20.22% of reference with a coverageData >= 1X There is a 8.15% of reference with a coverageData >= 2X There is a 3.43% of reference with a coverageData >= 3X There is a 1.65% of reference with a coverageData >= 4X There is a 0.85% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 98463605 0.3950385543873931 1.683487090573038 chr2 243199373 97851847 0.402352381887103 3.184558708932084 chr3 198022430 69728141 0.3521224388570527 0.90981434449174 chr4 191154276 57933662 0.3030728017823677 1.17517174785853 chr5 180915260 62162765 0.3436015568835929 0.896855589308952 chr6 171115067 63353332 0.3702381859804315 1.0509002237165057 chr7 159138663 57610182 0.3620124796448742 1.102596863130327 chr8 146364022 53566838 0.36598364316607807 1.0114143661051356 chr9 141213431 48638909 0.34443543121617093 1.4735531909809465 chr10 135534747 53797778 0.39692978509783916 1.9935830392039933 chr11 135006516 55322572 0.4097770510572986 1.4988878973826931 chr12 133851895 50198637 0.3750312014633786 1.016576356037889 chr13 115169878 30587804 0.2655885769020264 0.7734351272778748 chr14 107349540 34792477 0.3241045746446608 0.9151876764045334 chr15 102531392 39292700 0.38322604651656345 1.03422031405571 chr16 90354753 40096006 0.4437620010980496 2.089154801968022 chr17 81195210 35306522 0.4348350352194421 1.2001058517825547 chr18 78077248 27002079 0.3458379962367526 1.4545975186964681 chr19 59128983 25758886 0.43563891501397883 1.3886658629210815 chr20 63025520 28807811 0.45708168691031825 1.1642260482806508 chr21 48129895 13087316 0.27191657077165865 1.0884528154650022 chr22 51304566 18305615 0.3568028428502835 1.033914617256374 chrMT 16571 2580614 155.73073441554524 143.35869711988732 chrX 155270560 52644692 0.33905134366746664 0.9625885138440361 chrY 59373566 2476552 0.04171135686881263 1.2689832353418464