BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975311.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 68,124,124 number of mapped reads = 67,927,724 (99.71%) number of supplementary alignments = 110,217 (0.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 33,992,048 number of mapped paired reads (second in pair) = 33,935,676 number of mapped paired reads (both in pair) = 67,839,058 number of mapped paired reads (singletons) = 88,666 number of mapped bases = 6,341,125,044 bp number of sequenced bases = 6,338,958,199 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,465,197 duplication rate = 44.91% >>>>>>> Insert size mean insert size = 60,887.3271 std insert size = 2,442,945.9009 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 56.1552 >>>>>>> ACTG content number of A's = 1,674,643,340 bp (26.42%) number of C's = 1,417,617,695 bp (22.36%) number of T's = 1,719,009,410 bp (27.12%) number of G's = 1,527,427,031 bp (24.1%) number of N's = 260,723 bp (0%) GC percentage = 46.46% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 43,249,979 number of insertions = 604,725 mapped reads with insertion percentage = 0.88% number of deletions = 1,531,936 mapped reads with deletion percentage = 2.22% homopolymer indels = 47.55% >>>>>>> Coverage mean coverageData = 2.0484X std coverageData = 25.2074X There is a 13.99% of reference with a coverageData >= 1X There is a 6.94% of reference with a coverageData >= 2X There is a 4.11% of reference with a coverageData >= 3X There is a 3.15% of reference with a coverageData >= 4X There is a 2.6% of reference with a coverageData >= 5X There is a 2.32% of reference with a coverageData >= 6X There is a 2.14% of reference with a coverageData >= 7X There is a 2.01% of reference with a coverageData >= 8X There is a 1.91% of reference with a coverageData >= 9X There is a 1.83% of reference with a coverageData >= 10X There is a 1.76% of reference with a coverageData >= 11X There is a 1.7% of reference with a coverageData >= 12X There is a 1.65% of reference with a coverageData >= 13X There is a 1.6% of reference with a coverageData >= 14X There is a 1.56% of reference with a coverageData >= 15X There is a 1.52% of reference with a coverageData >= 16X There is a 1.48% of reference with a coverageData >= 17X There is a 1.45% of reference with a coverageData >= 18X There is a 1.41% of reference with a coverageData >= 19X There is a 1.38% of reference with a coverageData >= 20X There is a 1.35% of reference with a coverageData >= 21X There is a 1.33% of reference with a coverageData >= 22X There is a 1.3% of reference with a coverageData >= 23X There is a 1.27% of reference with a coverageData >= 24X There is a 1.25% of reference with a coverageData >= 25X There is a 1.23% of reference with a coverageData >= 26X There is a 1.21% of reference with a coverageData >= 27X There is a 1.18% of reference with a coverageData >= 28X There is a 1.16% of reference with a coverageData >= 29X There is a 1.14% of reference with a coverageData >= 30X There is a 1.13% of reference with a coverageData >= 31X There is a 1.11% of reference with a coverageData >= 32X There is a 1.09% of reference with a coverageData >= 33X There is a 1.07% of reference with a coverageData >= 34X There is a 1.06% of reference with a coverageData >= 35X There is a 1.04% of reference with a coverageData >= 36X There is a 1.02% of reference with a coverageData >= 37X There is a 1.01% of reference with a coverageData >= 38X There is a 0.99% of reference with a coverageData >= 39X There is a 0.98% of reference with a coverageData >= 40X There is a 0.97% of reference with a coverageData >= 41X There is a 0.95% of reference with a coverageData >= 42X There is a 0.94% of reference with a coverageData >= 43X There is a 0.93% of reference with a coverageData >= 44X There is a 0.92% of reference with a coverageData >= 45X There is a 0.9% of reference with a coverageData >= 46X There is a 0.89% of reference with a coverageData >= 47X There is a 0.88% of reference with a coverageData >= 48X There is a 0.87% of reference with a coverageData >= 49X There is a 0.86% of reference with a coverageData >= 50X There is a 0.85% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 712138193 2.8571170259993055 30.304947712779075 chr2 243199373 483894412 1.989702547465038 23.20510320424532 chr3 198022430 416965270 2.10564666841024 24.95515985611362 chr4 191154276 265441425 1.3886240504502239 19.678666682518045 chr5 180915260 304542189 1.6833416318778194 22.037637865037155 chr6 171115067 462924029 2.705337625236707 39.25096153401383 chr7 159138663 297256586 1.8679092836163893 22.413765870760876 chr8 146364022 236972060 1.6190594981053472 20.643817078783062 chr9 141213431 261130888 1.84919299921266 23.09451381295037 chr10 135534747 264942338 1.954792729277017 24.207473039900375 chr11 135006516 349096219 2.5857731118696523 27.040734427390372 chr12 133851895 354967274 2.6519405944906493 28.29910714264019 chr13 115169878 110934549 0.9632253756490043 15.333410312232088 chr14 107349540 216608115 2.017783355196492 25.099108047959586 chr15 102531392 238815086 2.329189932386756 26.37470357088951 chr16 90354753 218571217 2.4190339715720324 26.319590585895522 chr17 81195210 276690276 3.4077167359995744 30.708711261056028 chr18 78077248 111096739 1.4229079769819757 20.289884869046926 chr19 59128983 261893828 4.429195543579703 37.341068537971644 chr20 63025520 161240771 2.558340986317923 30.218091317880344 chr21 48129895 67154892 1.3952844069159096 19.608953020202065 chr22 51304566 109678605 2.1377942267360766 23.41448618781698 chrMT 16571 235318 14.200591394605032 25.117225716464784 chrX 155270560 146711970 0.944879505812306 13.581107976760078 chrY 59373566 11222795 0.1890200598697407 4.457026210273377