BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617357.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,632,022 (95.73%) number of supplementary alignments = 68,093 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,374,940 number of mapped paired reads (second in pair) = 15,257,082 number of mapped paired reads (both in pair) = 30,211,396 number of mapped paired reads (singletons) = 420,626 number of mapped bases = 3,015,527,076 bp number of sequenced bases = 3,014,622,702 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,593,023 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 58,481.868 std insert size = 2,306,839.401 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 53.5226 >>>>>>> ACTG content number of A's = 910,579,468 bp (30.21%) number of C's = 600,333,646 bp (19.91%) number of T's = 899,812,306 bp (29.85%) number of G's = 603,151,602 bp (20.01%) number of N's = 745,680 bp (0.02%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 28,189,075 number of insertions = 307,056 mapped reads with insertion percentage = 0.97% number of deletions = 372,694 mapped reads with deletion percentage = 1.18% homopolymer indels = 41.28% >>>>>>> Coverage mean coverageData = 0.9741X std coverageData = 9.916X There is a 53.76% of reference with a coverageData >= 1X There is a 24.46% of reference with a coverageData >= 2X There is a 9.44% of reference with a coverageData >= 3X There is a 3.32% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 196159246 0.7869960171533534 20.107357596366413 chr2 243199373 297499834 1.223275497507142 8.95883620909084 chr3 198022430 239274734 1.2083213704629319 1.475777962788635 chr4 191154276 164943913 0.8628837212095637 9.749364046728527 chr5 180915260 189204483 1.0458182632023412 1.462398948989564 chr6 171115067 140965431 0.8238049019961521 3.7298218279191135 chr7 159138663 244944633 1.539189964163517 10.878849483046476 chr8 146364022 126699647 0.8656474813188721 7.747086792089124 chr9 141213431 127057550 0.899755420573274 15.255770133576148 chr10 135534747 126707719 0.9348725828956614 20.217551760680287 chr11 135006516 161771982 1.198253142092786 5.6232716182025735 chr12 133851895 132921443 0.9930486452956082 1.373860714057128 chr13 115169878 131167093 1.1389010327856735 1.3000685173911024 chr14 107349540 87041585 0.8108240147093317 1.3773656205916929 chr15 102531392 67966047 0.6628803693604394 0.985193057228961 chr16 90354753 76101509 0.8422524158745694 7.90483203942468 chr17 81195210 94523014 1.1641452001909964 7.373388821562635 chr18 78077248 54573492 0.6989679246891489 15.645528949488943 chr19 59128983 56712341 0.9591293156521904 9.618071597963814 chr20 63025520 86871892 1.3783605752082648 2.5065470739136475 chr21 48129895 47854847 0.9942852981499336 3.2317931431276254 chr22 51304566 27083785 0.5279020389725156 0.9262946991445191 chrMT 16571 2079567 125.49435761269687 19.40107501732681 chrX 155270560 125019096 0.8051693508415246 3.0492741951829356 chrY 59373566 10382193 0.17486221056690446 8.55027043951024