BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231716.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 = 569,350 number of mapped reads = 92,236 (16.2%) number of supplementary alignments = 810 (0.14%) number of secondary alignments = 0 number of mapped bases = 5,550,633 bp number of sequenced bases = 5,547,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,299 duplication rate = 6.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9543 >>>>>>> ACTG content number of A's = 1,489,408 bp (26.85%) number of C's = 918,016 bp (16.55%) number of T's = 1,885,095 bp (33.98%) number of G's = 1,255,150 bp (22.62%) number of N's = 249 bp (0%) GC percentage = 39.17% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 52,249 number of insertions = 836 mapped reads with insertion percentage = 0.88% number of deletions = 1,530 mapped reads with deletion percentage = 1.63% homopolymer indels = 39.69% >>>>>>> Coverage mean coverageData = 0.0018X std coverageData = 0.0747X There is a 0.14% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 434497 0.001743213309787501 0.05859405987527145 chr2 243199373 476640 0.001959873473851431 0.06585925474363984 chr3 198022430 418526 0.002113528250309826 0.06071582672203909 chr4 191154276 435101 0.0022761771753408225 0.06748674220948749 chr5 180915260 342186 0.0018914159037772711 0.05930748739826123 chr6 171115067 336496 0.0019664896019939613 0.08300704873835284 chr7 159138663 291520 0.0018318615633964451 0.07508069986502042 chr8 146364022 293140 0.002002814598795324 0.0660198603064436 chr9 141213431 210234 0.0014887677362644066 0.049443468357595506 chr10 135534747 275394 0.002031906991348868 0.05859875604733103 chr11 135006516 230204 0.0017051325137521511 0.0540271439140384 chr12 133851895 248641 0.0018575829651122982 0.08713396497595817 chr13 115169878 208709 0.0018121839114911627 0.062223183479113764 chr14 107349540 182855 0.0017033608155190977 0.053559220255776925 chr15 102531392 134352 0.0013103499072752275 0.08644290742979292 chr16 90354753 139391 0.001542707996777989 0.05061952109913235 chr17 81195210 128522 0.0015828766253575795 0.052003673543122075 chr18 78077248 161238 0.002065108647271994 0.25902775057706806 chr19 59128983 100098 0.0016928753873544553 0.050387865692769984 chr20 63025520 103470 0.0016417159271355476 0.05226210424547692 chr21 48129895 69131 0.001436342215165855 0.04836857224468438 chr22 51304566 49137 9.57751011869002E-4 0.03866589952823902 chrMT 16571 3096 0.18683241807977793 0.5413511060789878 chrX 155270560 253566 0.001633059093752222 0.05354326605024088 chrY 59373566 24489 4.1245627725981624E-4 0.025410765236030503