BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617701.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 42,262,156 number of mapped reads = 41,123,477 (97.31%) number of supplementary alignments = 2,118,737 (5.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,785,804 number of mapped paired reads (second in pair) = 20,337,673 number of mapped paired reads (both in pair) = 40,433,446 number of mapped paired reads (singletons) = 690,031 number of mapped bases = 5,543,677,401 bp number of sequenced bases = 5,539,924,001 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,838,866 duplication rate = 13.74% >>>>>>> Insert size mean insert size = 442,645.0542 std insert size = 6,588,732.8179 median insert size = 286 >>>>>>> Mapping quality mean mapping quality = 52.0507 >>>>>>> ACTG content number of A's = 1,562,774,328 bp (28.21%) number of C's = 1,123,530,428 bp (20.28%) number of T's = 1,579,422,681 bp (28.51%) number of G's = 1,274,107,881 bp (23%) number of N's = 88,683 bp (0%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 75,809,047 number of insertions = 1,000,830 mapped reads with insertion percentage = 2.26% number of deletions = 1,729,280 mapped reads with deletion percentage = 4.02% homopolymer indels = 42.64% >>>>>>> Coverage mean coverageData = 1.7908X std coverageData = 29.2984X There is a 43.88% of reference with a coverageData >= 1X There is a 29.45% of reference with a coverageData >= 2X There is a 20.62% of reference with a coverageData >= 3X There is a 15.09% of reference with a coverageData >= 4X There is a 11.29% of reference with a coverageData >= 5X There is a 8.62% of reference with a coverageData >= 6X There is a 6.68% of reference with a coverageData >= 7X There is a 5.25% of reference with a coverageData >= 8X There is a 4.17% of reference with a coverageData >= 9X There is a 3.34% of reference with a coverageData >= 10X There is a 2.7% of reference with a coverageData >= 11X There is a 2.2% of reference with a coverageData >= 12X There is a 1.81% of reference with a coverageData >= 13X There is a 1.5% of reference with a coverageData >= 14X There is a 1.25% of reference with a coverageData >= 15X There is a 1.04% of reference with a coverageData >= 16X There is a 0.88% of reference with a coverageData >= 17X There is a 0.74% of reference with a coverageData >= 18X There is a 0.63% of reference with a coverageData >= 19X There is a 0.54% of reference with a coverageData >= 20X There is a 0.46% of reference with a coverageData >= 21X There is a 0.4% of reference with a coverageData >= 22X There is a 0.35% of reference with a coverageData >= 23X There is a 0.3% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 597140593 2.395743651928554 40.62486697210483 chr2 243199373 426369684 1.7531693389686493 35.18058321881329 chr3 198022430 362847325 1.8323546731549551 4.36532808797629 chr4 191154276 148649753 0.777642834419252 21.331308775297664 chr5 180915260 317328013 1.7540146309382636 4.410962514541492 chr6 171115067 288740187 1.6874036404988229 14.060226097312015 chr7 159138663 429937274 2.701651917233966 42.35798493329965 chr8 146364022 264184901 1.8049852510885496 9.036871971963802 chr9 141213431 313063303 2.216951325260272 48.5638878553851 chr10 135534747 305317433 2.25268751931193 72.44974879276272 chr11 135006516 253713130 1.8792658126219626 15.061667918258195 chr12 133851895 229612969 1.715425612764018 6.724175069049143 chr13 115169878 97196061 0.8439364761678396 2.0995565809474455 chr14 107349540 124354846 1.1584106089322785 3.297423315265456 chr15 102531392 152490005 1.487251875015995 4.786181221597892 chr16 90354753 237773829 2.6315586187259012 48.398252756056685 chr17 81195210 120868592 1.4886172718809398 21.37553802973993 chr18 78077248 144719158 1.8535381523693049 34.21102455042575 chr19 59128983 144346373 2.441211833459067 24.922588441602837 chr20 63025520 169395713 2.687732096458704 7.873671701807063 chr21 48129895 76500619 1.5894615809986703 11.172596258890266 chr22 51304566 54456407 1.06143392773267 3.2155549256771936 chrMT 16571 849361 51.25586868625913 29.69086068597176 chrX 155270560 263013612 1.693905219379643 9.096813958241377 chrY 59373566 20808260 0.3504633695068947 23.607568614006603