BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006076.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 9,246,460 number of mapped reads = 7,859,417 (85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,999,363 number of mapped paired reads (second in pair) = 3,860,054 number of mapped paired reads (both in pair) = 7,039,918 number of mapped paired reads (singletons) = 819,499 number of mapped bases = 302,935,062 bp number of sequenced bases = 302,901,632 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 579,661 duplication rate = 6.73% >>>>>>> Insert size mean insert size = 76,066.9082 std insert size = 2,745,426.9249 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 46.466 >>>>>>> ACTG content number of A's = 80,675,954 bp (26.63%) number of C's = 66,901,470 bp (22.09%) number of T's = 83,784,219 bp (27.66%) number of G's = 71,527,820 bp (23.61%) number of N's = 12,169 bp (0%) GC percentage = 45.7% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,525,849 number of insertions = 10,354 mapped reads with insertion percentage = 0.13% number of deletions = 26,528 mapped reads with deletion percentage = 0.34% homopolymer indels = 45.18% >>>>>>> Coverage mean coverageData = 0.0979X std coverageData = 0.571X There is a 5.22% of reference with a coverageData >= 1X There is a 2.39% of reference with a coverageData >= 2X There is a 1.11% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 26156934 0.10494230223001129 0.6406952845112638 chr2 243199373 26446626 0.10874463068619836 0.6293109591685435 chr3 198022430 20502622 0.10353686701046948 0.5267092638709429 chr4 191154276 18100574 0.09469091865881148 0.522234904603068 chr5 180915260 18092085 0.1000030898443835 0.5184606925979751 chr6 171115067 17125914 0.10008419655996745 0.5988279709030107 chr7 159138663 16652468 0.10464124610623378 0.6601758826122361 chr8 146364022 15010851 0.10255833909784196 0.6022913182297924 chr9 141213431 12845329 0.0909639324605037 0.5217606719103226 chr10 135534747 14781180 0.10905823286776785 0.5624524777619484 chr11 135006516 13920701 0.10311132686366042 0.7695729112406848 chr12 133851895 13929169 0.10406404033353431 0.5328667853082366 chr13 115169878 9128455 0.0792607855328283 0.4646139097630889 chr14 107349540 9458511 0.08810946930932355 0.49690440436002653 chr15 102531392 9279977 0.09050864149001313 0.5006527164017515 chr16 90354753 9817264 0.10865243580489894 0.5718097698579877 chr17 81195210 9645781 0.11879741428096559 0.6103380520164347 chr18 78077248 7654344 0.09803552502260325 0.5945598224353112 chr19 59128983 7358687 0.12445143864557928 0.6870746706787195 chr20 63025520 7353465 0.11667440427306272 0.5735500399793109 chr21 48129895 4029119 0.0837134383941623 0.5156009832994741 chr22 51304566 4556078 0.08880453252445406 0.5110440307567463 chrMT 16571 26696 1.611007181220204 2.502402253913437 chrX 155270560 9101236 0.05861533570819864 0.4062100518525043 chrY 59373566 1960996 0.03302809873336562 0.3177521296318444