BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472468.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 12,282,660 number of mapped reads = 12,123,012 (98.7%) number of supplementary alignments = 40,743 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,096,183 number of mapped paired reads (second in pair) = 6,026,829 number of mapped paired reads (both in pair) = 12,038,654 number of mapped paired reads (singletons) = 84,358 number of mapped bases = 1,184,091,434 bp number of sequenced bases = 1,183,951,422 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,476,046 duplication rate = 44.15% >>>>>>> Insert size mean insert size = 18,171.3216 std insert size = 1,342,024.457 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 55.134 >>>>>>> ACTG content number of A's = 320,382,820 bp (27.06%) number of C's = 271,631,308 bp (22.94%) number of T's = 322,419,235 bp (27.23%) number of G's = 269,358,691 bp (22.75%) number of N's = 159,368 bp (0.01%) GC percentage = 45.69% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 5,276,120 number of insertions = 74,096 mapped reads with insertion percentage = 0.6% number of deletions = 56,887 mapped reads with deletion percentage = 0.46% homopolymer indels = 45.6% >>>>>>> Coverage mean coverageData = 0.3825X std coverageData = 9.9676X There is a 3.79% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 140327881 0.5629991228788153 13.537608941537483 chr2 243199373 92144486 0.37888455411437266 10.124601056956456 chr3 198022430 88519523 0.44701765855514447 8.758083732527178 chr4 191154276 43220004 0.22610011611772682 7.991288919259698 chr5 180915260 60054218 0.3319466693964898 9.886357294251473 chr6 171115067 92599336 0.5411524398374574 10.506223295770416 chr7 159138663 79770977 0.5012671056561535 13.540767691740204 chr8 146364022 72585885 0.49592710017219943 11.30611957964478 chr9 141213431 52263282 0.37010135388609033 9.839880816267685 chr10 135534747 25299453 0.18666396300573757 5.005656724325488 chr11 135006516 43048310 0.31886098001373503 8.711207728704956 chr12 133851895 49080050 0.36667430072618695 7.701407431994408 chr13 115169878 34138680 0.29642021501490173 8.948287611067792 chr14 107349540 31338896 0.2919332118237302 8.949422346606994 chr15 102531392 26478134 0.25824416779594683 6.993816026693263 chr16 90354753 60044928 0.6645464240270791 16.560223262890656 chr17 81195210 48165476 0.5932058800020346 12.320798650148678 chr18 78077248 15066255 0.19296600976509828 5.692644344438003 chr19 59128983 26533130 0.44873306885728104 8.669464464526518 chr20 63025520 30080842 0.47728034612011133 11.202592425596334 chr21 48129895 8490100 0.17639971996614578 9.586749469605387 chr22 51304566 14859136 0.28962599547182605 7.566599696480548 chrMT 16571 8777 0.5296602498340475 1.0562643632717001 chrX 155270560 48913283 0.3150196856377667 6.987004387111884 chrY 59373566 1060392 0.01785966502332031 0.721147021734422