BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234066.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 = 6,286,293 number of mapped reads = 5,877,517 (93.5%) number of supplementary alignments = 40,025 (0.64%) number of secondary alignments = 0 number of mapped bases = 396,262,245 bp number of sequenced bases = 396,125,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 584,294 duplication rate = 4.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6153 >>>>>>> ACTG content number of A's = 104,663,095 bp (26.42%) number of C's = 73,285,053 bp (18.5%) number of T's = 114,971,906 bp (29.02%) number of G's = 103,118,846 bp (26.03%) number of N's = 86,332 bp (0.02%) GC percentage = 44.53% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,610,298 number of insertions = 27,412 mapped reads with insertion percentage = 0.46% number of deletions = 84,944 mapped reads with deletion percentage = 1.43% homopolymer indels = 46.22% >>>>>>> Coverage mean coverageData = 0.128X std coverageData = 33.667X There is a 8.47% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 38222903 0.15335128493019884 1.9823109209759973 chr2 243199373 45064107 0.1852969703174358 120.06369947407816 chr3 198022430 30546673 0.15425865140630787 0.5388162652551107 chr4 191154276 16098425 0.08421692329812178 0.44460725294185893 chr5 180915260 28010985 0.15482931069496295 0.5485392077717075 chr6 171115067 23540290 0.13756994292033908 0.6887010253382007 chr7 159138663 21725441 0.13651893631907666 1.805847206430233 chr8 146364022 17237513 0.11777151764796406 1.2125578422462258 chr9 141213431 14918387 0.10564424994390229 0.9242252116163181 chr10 135534747 13179120 0.097237942975612 0.7564007067402785 chr11 135006516 15138341 0.11213044709634608 1.0698080639355954 chr12 133851895 10053699 0.07511062133263037 0.4049166708952769 chr13 115169878 12980803 0.11271005253648007 0.4553583336608256 chr14 107349540 17110294 0.15938861032846532 0.7560009211025986 chr15 102531392 8788506 0.08571527049978996 0.40482237470821036 chr16 90354753 11280257 0.12484409093564784 0.6112133736108634 chr17 81195210 11320825 0.1394272519277923 0.6821429235284459 chr18 78077248 7810962 0.10004146150233163 2.1041454048897443 chr19 59128983 10179240 0.17215313850400574 1.3677224801952415 chr20 63025520 9375162 0.148751838937624 0.588510584325629 chr21 48129895 6689625 0.13899105742906773 0.5896042106926221 chr22 51304566 4169395 0.08126752305048249 0.39485939028294603 chrMT 16571 27300 1.647456399734476 1.9940288570110405 chrX 155270560 21478694 0.13833075632624756 0.6626541367152431 chrY 59373566 1315298 0.022152922396475226 0.28483059144137496