BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063595.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 = 1,947,506 number of mapped reads = 1,610,275 (82.68%) number of supplementary alignments = 9,253 (0.48%) number of secondary alignments = 0 number of mapped bases = 102,464,770 bp number of sequenced bases = 102,410,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 257,437 duplication rate = 12.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3009 >>>>>>> ACTG content number of A's = 27,746,931 bp (27.09%) number of C's = 18,237,117 bp (17.81%) number of T's = 33,555,973 bp (32.77%) number of G's = 22,867,694 bp (22.33%) number of N's = 2,496 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 946,847 number of insertions = 7,037 mapped reads with insertion percentage = 0.43% number of deletions = 31,147 mapped reads with deletion percentage = 1.91% homopolymer indels = 49.26% >>>>>>> Coverage mean coverageData = 0.0331X std coverageData = 0.3891X There is a 1.67% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 11887765 0.04769402359884191 0.657681140061996 chr2 243199373 10626032 0.04369267843466027 0.40005546871268194 chr3 198022430 5851427 0.029549314186276775 0.29065684988602475 chr4 191154276 6274701 0.0328253237714651 0.30717923741319486 chr5 180915260 5512627 0.0304707684691717 0.29294462731340465 chr6 171115067 5823737 0.03403403979615658 0.32927499191287285 chr7 159138663 7233899 0.04545657770167392 0.6270280793707218 chr8 146364022 4286416 0.02928599488745943 0.457600266895557 chr9 141213431 3577712 0.025335493760504976 0.31681320351673564 chr10 135534747 5761236 0.042507446448400425 0.40519934217290526 chr11 135006516 5478513 0.040579619134827535 0.38515218640166016 chr12 133851895 3338698 0.024943225495612148 0.26683328460867234 chr13 115169878 3045222 0.026441132463472784 0.2743303076049392 chr14 107349540 2337582 0.021775426331589312 0.2655424810421984 chr15 102531392 1859282 0.018133782871103517 0.22270007418453303 chr16 90354753 2544735 0.028163820004023475 0.2850617498883481 chr17 81195210 2475794 0.03049187261169717 0.29931461467336695 chr18 78077248 2202526 0.02820957521453625 0.4400213820304168 chr19 59128983 2202583 0.037250480022631205 0.46052173943544855 chr20 63025520 1769716 0.028079355791114455 0.28540939973789914 chr21 48129895 1699634 0.03531347824465439 0.32404441688964714 chr22 51304566 1132610 0.02207620273018195 0.24539355722834394 chrMT 16571 51615 3.1147788304869954 4.038696571638488 chrX 155270560 5286296 0.03404570705483383 0.31924319828445386 chrY 59373566 204412 0.003442811570388075 0.09891789535430758