BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717001.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 = 2,761,646 number of mapped reads = 2,535,957 (91.83%) number of supplementary alignments = 12,154 (0.44%) number of secondary alignments = 0 number of mapped bases = 147,124,764 bp number of sequenced bases = 147,084,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,642 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6539 >>>>>>> ACTG content number of A's = 36,347,409 bp (24.71%) number of C's = 27,526,495 bp (18.71%) number of T's = 46,766,632 bp (31.8%) number of G's = 36,441,319 bp (24.78%) number of N's = 2,168 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 765,053 number of insertions = 8,962 mapped reads with insertion percentage = 0.35% number of deletions = 24,587 mapped reads with deletion percentage = 0.96% homopolymer indels = 42.82% >>>>>>> Coverage mean coverageData = 0.0475X std coverageData = 0.4352X There is a 4.09% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 10589926 0.042487059641067054 0.7985689434136778 chr2 243199373 11315383 0.04652718820948605 0.4907490645147701 chr3 198022430 8513290 0.04299154393772463 0.23089687012524165 chr4 191154276 9838955 0.05147127862313684 0.28422065043167855 chr5 180915260 8223385 0.0454543469688516 0.24425841799021258 chr6 171115067 7623483 0.04455179274189806 0.27455914417363253 chr7 159138663 9231606 0.05800982505426729 0.5932653864246397 chr8 146364022 6283894 0.04293332414710495 0.41970244745505175 chr9 141213431 6693185 0.04739765157324164 0.46484798351868367 chr10 135534747 5699735 0.04205368089114447 0.4008132358465458 chr11 135006516 5666616 0.04197290744100085 0.36019875697346 chr12 133851895 10994267 0.08213755210563138 0.37652073282533044 chr13 115169878 5523666 0.04796103022701821 0.24318701147580377 chr14 107349540 6181235 0.057580451672172975 0.31186267238251736 chr15 102531392 3733339 0.0364116679504361 0.21418886411756552 chr16 90354753 4058086 0.04491281161490199 0.27750397175314706 chr17 81195210 4350438 0.053579983351234636 0.27380600982765796 chr18 78077248 4587185 0.05875187865228037 0.9003089461386021 chr19 59128983 2497029 0.04223020375642179 0.6080638156949629 chr20 63025520 4492846 0.07128613932895754 0.3141874581988208 chr21 48129895 1748818 0.03633537949750358 0.25428962897679236 chr22 51304566 1375663 0.02681365631277341 0.1802766353487995 chrMT 16571 15200 0.9172651016836643 1.133290576634332 chrX 155270560 7496297 0.048278933237569314 0.3168085446526399 chrY 59373566 391237 0.006589413881591683 0.14982753236015792