BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525171.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,259,923 number of mapped reads = 2,087,314 (92.36%) number of supplementary alignments = 8,210 (0.36%) number of secondary alignments = 0 number of mapped bases = 122,079,221 bp number of sequenced bases = 122,040,703 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,916 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7898 >>>>>>> ACTG content number of A's = 28,938,291 bp (23.71%) number of C's = 22,987,978 bp (18.84%) number of T's = 39,135,654 bp (32.07%) number of G's = 30,976,300 bp (25.38%) number of N's = 2,480 bp (0%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 618,131 number of insertions = 8,599 mapped reads with insertion percentage = 0.41% number of deletions = 23,667 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.0394X std coverageData = 0.3496X There is a 3.46% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10252976 0.04113520744247213 0.5490458492797742 chr2 243199373 9721810 0.0399746507570149 0.5270216257648134 chr3 198022430 6989374 0.0352958702708577 0.21031861975671204 chr4 191154276 7428692 0.03886228524649901 0.27839119242130167 chr5 180915260 6906612 0.03817595044221256 0.217144337863574 chr6 171115067 6501554 0.03799521640020163 0.26424073907489165 chr7 159138663 7012448 0.044065017688379095 0.46118380242847345 chr8 146364022 6387863 0.04364366948046836 0.46530062734780225 chr9 141213431 4067542 0.02880421480588486 0.24429075792413346 chr10 135534747 5449367 0.04020642027686081 0.37736948248077123 chr11 135006516 4335577 0.03211383515740825 0.2637852828011969 chr12 133851895 5961126 0.04453523799569666 0.23790405396594197 chr13 115169878 3617750 0.031412293412345194 0.1986012390635448 chr14 107349540 4079108 0.03799837428274029 0.22275196445957396 chr15 102531392 4501759 0.04390615315161234 0.23471069328162036 chr16 90354753 4222102 0.046728056464279195 0.2570085005330295 chr17 81195210 5377495 0.06622921475293925 0.3054492298487653 chr18 78077248 2253325 0.028860200093118037 0.42124758800375034 chr19 59128983 3198323 0.054090614073304795 0.436975832676677 chr20 63025520 4081946 0.06476655805457852 0.2987246272355512 chr21 48129895 1593902 0.03311667311968996 0.26789614463669836 chr22 51304566 1155376 0.022519944910946135 0.16720554612588878 chrMT 16571 6213 0.37493211031319773 0.7058274806777366 chrX 155270560 6521584 0.04200141997298135 0.2493174007730105 chrY 59373566 455397 0.007670029453848199 0.3353762389315312