BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153310.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 47,978,346 number of mapped reads = 47,599,566 (99.21%) number of supplementary alignments = 247,024 (0.51%) number of secondary alignments = 0 number of mapped bases = 4,621,815,805 bp number of sequenced bases = 4,621,251,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,482,389 duplication rate = 61.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.4924 >>>>>>> ACTG content number of A's = 1,211,691,353 bp (26.22%) number of C's = 1,091,842,679 bp (23.63%) number of T's = 1,246,928,923 bp (26.98%) number of G's = 1,069,267,374 bp (23.14%) number of N's = 1,521,621 bp (0.03%) GC percentage = 46.76% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 12,801,766 number of insertions = 321,377 mapped reads with insertion percentage = 0.67% number of deletions = 279,067 mapped reads with deletion percentage = 0.58% homopolymer indels = 49.7% >>>>>>> Coverage mean coverageData = 1.493X std coverageData = 15.7383X There is a 9.31% of reference with a coverageData >= 1X There is a 6.73% of reference with a coverageData >= 2X There is a 4.72% of reference with a coverageData >= 3X There is a 3.98% of reference with a coverageData >= 4X There is a 3.2% of reference with a coverageData >= 5X There is a 2.94% of reference with a coverageData >= 6X There is a 2.58% of reference with a coverageData >= 7X There is a 2.43% of reference with a coverageData >= 8X There is a 2.24% of reference with a coverageData >= 9X There is a 2.13% of reference with a coverageData >= 10X There is a 2.02% of reference with a coverageData >= 11X There is a 1.94% of reference with a coverageData >= 12X There is a 1.85% of reference with a coverageData >= 13X There is a 1.79% of reference with a coverageData >= 14X There is a 1.72% of reference with a coverageData >= 15X There is a 1.67% of reference with a coverageData >= 16X There is a 1.61% of reference with a coverageData >= 17X There is a 1.56% of reference with a coverageData >= 18X There is a 1.51% of reference with a coverageData >= 19X There is a 1.47% of reference with a coverageData >= 20X There is a 1.43% of reference with a coverageData >= 21X There is a 1.39% of reference with a coverageData >= 22X There is a 1.35% of reference with a coverageData >= 23X There is a 1.32% of reference with a coverageData >= 24X There is a 1.28% of reference with a coverageData >= 25X There is a 1.25% of reference with a coverageData >= 26X There is a 1.22% of reference with a coverageData >= 27X There is a 1.19% 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 1.11% of reference with a coverageData >= 31X There is a 1.08% of reference with a coverageData >= 32X There is a 1.06% of reference with a coverageData >= 33X There is a 1.04% of reference with a coverageData >= 34X There is a 1.01% of reference with a coverageData >= 35X There is a 0.99% of reference with a coverageData >= 36X There is a 0.97% of reference with a coverageData >= 37X There is a 0.95% of reference with a coverageData >= 38X There is a 0.93% of reference with a coverageData >= 39X There is a 0.91% of reference with a coverageData >= 40X There is a 0.89% of reference with a coverageData >= 41X There is a 0.88% of reference with a coverageData >= 42X There is a 0.86% of reference with a coverageData >= 43X There is a 0.84% of reference with a coverageData >= 44X There is a 0.83% of reference with a coverageData >= 45X There is a 0.81% of reference with a coverageData >= 46X There is a 0.8% of reference with a coverageData >= 47X There is a 0.78% of reference with a coverageData >= 48X There is a 0.77% of reference with a coverageData >= 49X There is a 0.75% of reference with a coverageData >= 50X There is a 0.74% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 490482748 1.9678295926893599 18.23810521834734 chr2 243199373 346229429 1.4236444145766773 13.481323857424737 chr3 198022430 240020800 1.21208895376145 11.880491919277445 chr4 191154276 190291476 0.9954863682986616 11.488220140866177 chr5 180915260 291337606 1.6103539635075559 16.48912177908027 chr6 171115067 163436981 0.9551291061937871 10.153677899548173 chr7 159138663 212402672 1.334701875684352 13.483989155315728 chr8 146364022 244480743 1.6703609238068082 26.145140280476575 chr9 141213431 120989577 0.8567851948870218 9.266781472926155 chr10 135534747 234176556 1.7277971972751756 16.534528308876904 chr11 135006516 215588999 1.5968784721472258 14.41336311791924 chr12 133851895 229427999 1.7140437122686982 14.878899184058495 chr13 115169878 61817201 0.5367479941239497 7.621501650357963 chr14 107349540 137134047 1.2774535130751374 12.502575778176938 chr15 102531392 213638025 2.0836352733804686 18.357970500068145 chr16 90354753 215834207 2.388742150620455 22.262690734938175 chr17 81195210 192112481 2.366056827736513 17.440211526205385 chr18 78077248 49756901 0.6372778533382734 7.720057870673306 chr19 59128983 223505399 3.779963524825042 27.097579719032524 chr20 63025520 121565781 1.9288342404790948 19.026436194783827 chr21 48129895 48829565 1.0145371187699455 11.550725845474673 chr22 51304566 65739817 1.2813638653526471 12.524649853964348 chrMT 16571 20292 1.2245489107476917 3.761582827881915 chrX 155270560 310443589 1.999371864183397 21.18888490892532 chrY 59373566 2552914 0.04299748477293751 1.6520573529102336