BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240031.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,246,241 number of mapped reads = 968,537 (77.72%) number of supplementary alignments = 3,773 (0.3%) number of secondary alignments = 0 number of mapped bases = 59,543,698 bp number of sequenced bases = 59,506,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,041 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1669 >>>>>>> ACTG content number of A's = 16,343,853 bp (27.47%) number of C's = 9,953,280 bp (16.73%) number of T's = 18,969,062 bp (31.88%) number of G's = 14,202,924 bp (23.87%) number of N's = 37,333 bp (0.06%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 640,556 number of insertions = 4,703 mapped reads with insertion percentage = 0.48% number of deletions = 21,731 mapped reads with deletion percentage = 2.21% homopolymer indels = 49.66% >>>>>>> Coverage mean coverageData = 0.0192X std coverageData = 0.2102X There is a 1.67% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 4393591 0.01762720181948915 0.2644524181467008 chr2 243199373 6153737 0.02530326013628333 0.2543537255428761 chr3 198022430 4061924 0.020512443969099865 0.1643701578779015 chr4 191154276 3804002 0.019900166920670925 0.1654912241469571 chr5 180915260 3387263 0.018722925860427696 0.1566235556308114 chr6 171115067 3412713 0.019943965542204418 0.18202985498141053 chr7 159138663 3511922 0.022068314096618996 0.38421993269952104 chr8 146364022 3657694 0.024990390056376013 0.2565815799366128 chr9 141213431 2154380 0.015256197549650925 0.19856653092542967 chr10 135534747 2624074 0.019360894959283025 0.17759376219718423 chr11 135006516 2800156 0.020740895202421193 0.2173093666989521 chr12 133851895 2795949 0.020888378158560997 0.16533022520825782 chr13 115169878 1448833 0.012579964702228824 0.12702740983369382 chr14 107349540 2134746 0.019885935235493323 0.1684100622562726 chr15 102531392 1485179 0.014485114958743562 0.14732314185705614 chr16 90354753 1595501 0.017658185618635913 0.15411183413275542 chr17 81195210 1575867 0.019408373966887948 0.16819042307042828 chr18 78077248 1379471 0.017668027950985158 0.2938506606451068 chr19 59128983 1009342 0.01707017352217947 0.20360183596057743 chr20 63025520 1197214 0.018995702058467744 0.15949467568181194 chr21 48129895 939235 0.01951458651634291 0.16334538351504532 chr22 51304566 579249 0.01129039859727105 0.12212980161672048 chrMT 16571 38635 2.331482710759761 2.8296406935627654 chrX 155270560 3262074 0.021008966542015433 0.18014729816810995 chrY 59373566 140947 0.0023739015439968687 0.06055478855927197