BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818801.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 = 1,565,663 number of mapped reads = 1,512,824 (96.63%) number of supplementary alignments = 11,471 (0.73%) number of secondary alignments = 0 number of mapped bases = 102,677,980 bp number of sequenced bases = 102,634,453 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 643,507 duplication rate = 36.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6977 >>>>>>> ACTG content number of A's = 29,755,842 bp (28.99%) number of C's = 21,839,234 bp (21.28%) number of T's = 29,821,728 bp (29.06%) number of G's = 21,211,215 bp (20.67%) number of N's = 6,434 bp (0.01%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 525,260 number of insertions = 12,884 mapped reads with insertion percentage = 0.84% number of deletions = 26,378 mapped reads with deletion percentage = 1.72% homopolymer indels = 39.97% >>>>>>> Coverage mean coverageData = 0.0332X std coverageData = 0.451X There is a 1.65% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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% 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 8475637 0.034004476963770534 0.5917928652667094 chr2 243199373 9118472 0.03749381376900178 0.8072711385524528 chr3 198022430 7070399 0.03570504109054717 0.3338130780981062 chr4 191154276 6771001 0.035421655961282286 0.36904888788348184 chr5 180915260 6400060 0.035376009740692965 0.3414347785817034 chr6 171115067 6018634 0.03517302190577993 0.36951317052213145 chr7 159138663 5597291 0.03517241438681686 0.3883401781804538 chr8 146364022 5306520 0.03625563118236803 0.37287596278197543 chr9 141213431 4396712 0.03113522537385272 0.3689550156124239 chr10 135534747 5033165 0.03713560626633995 0.4703173157400859 chr11 135006516 4807578 0.03560997011433137 0.3741583851769649 chr12 133851895 4746612 0.03546167202190152 0.3619778096368772 chr13 115169878 3282835 0.028504284774878375 0.2984943868546984 chr14 107349540 3173676 0.029563945965674375 0.3375254726159404 chr15 102531392 3002979 0.029288386136413713 0.30533290922608003 chr16 90354753 3086528 0.03416010666312153 0.5444953286647807 chr17 81195210 2730462 0.033628363052451 0.34631091496407784 chr18 78077248 2797357 0.035828068632746894 0.4555332732407233 chr19 59128983 2028981 0.03431449176117235 0.5301539085135887 chr20 63025520 2230614 0.03539223476458425 0.35822295778611357 chr21 48129895 1414453 0.029388241964791322 0.3172272990725616 chr22 51304566 1242868 0.024225290201265907 0.2986348398155185 chrMT 16571 16423 0.991068734536238 1.997353238898535 chrX 155270560 3001392 0.01933007776876698 0.27544740973657533 chrY 59373566 927331 0.015618583529242626 0.7183114082137084