BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234106.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 = 5,463,668 number of mapped reads = 5,171,093 (94.65%) number of supplementary alignments = 35,641 (0.65%) number of secondary alignments = 0 number of mapped bases = 355,989,689 bp number of sequenced bases = 355,873,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 476,547 duplication rate = 4.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2551 >>>>>>> ACTG content number of A's = 95,074,846 bp (26.72%) number of C's = 67,267,584 bp (18.9%) number of T's = 103,419,242 bp (29.06%) number of G's = 90,032,820 bp (25.3%) number of N's = 79,271 bp (0.02%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 2,189,522 number of insertions = 23,596 mapped reads with insertion percentage = 0.45% number of deletions = 71,048 mapped reads with deletion percentage = 1.36% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.115X std coverageData = 26.0194X There is a 7.71% of reference with a coverageData >= 1X There is a 2.14% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.22% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 26855881 0.10774649584524004 1.5888966871018202 chr2 243199373 41933023 0.17242241409890477 92.78419774662979 chr3 198022430 22791692 0.11509651709657336 0.4560886518833502 chr4 191154276 21752829 0.11379723987968754 0.485412481284947 chr5 180915260 21963498 0.1214021304781034 0.47055940774421695 chr6 171115067 19976522 0.11674320882567285 0.6162040141239167 chr7 159138663 19052020 0.1197196183557229 1.60837838380144 chr8 146364022 17247422 0.1178392187118225 0.8651679311210502 chr9 141213431 14300558 0.10126910661918553 0.8177990157878043 chr10 135534747 15828897 0.11678847934102095 0.6902036924307218 chr11 135006516 15355078 0.11373582886917843 0.7832254233776145 chr12 133851895 15561135 0.11625636678509482 0.4777988513752291 chr13 115169878 10761573 0.09344086480668148 0.4108163749327508 chr14 107349540 10216056 0.09516627644608444 0.5895126424461584 chr15 102531392 10137282 0.09887003192154067 0.4250242583764982 chr16 90354753 9657218 0.1068811288765296 0.5175715640430072 chr17 81195210 9309357 0.11465401715199702 0.565757520050271 chr18 78077248 9235387 0.11828525257447599 1.6427829200850947 chr19 59128983 7074955 0.11965291200763592 1.1293668050084475 chr20 63025520 7577222 0.12022466454858285 0.49254895032434604 chr21 48129895 4564753 0.09484236356634479 0.5047309956129555 chr22 51304566 4020448 0.07836433115914089 0.3762522253988499 chrMT 16571 334600 20.191901514694347 11.807176372420535 chrX 155270560 19697790 0.12686107398595073 0.5752311242466585 chrY 59373566 784493 0.013212832794984893 0.22551843426626564