BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716381.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 = 1,017,064 number of mapped reads = 930,502 (91.49%) number of supplementary alignments = 3,883 (0.38%) number of secondary alignments = 0 number of mapped bases = 53,480,709 bp number of sequenced bases = 53,466,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,037 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5044 >>>>>>> ACTG content number of A's = 12,730,798 bp (23.81%) number of C's = 9,875,106 bp (18.47%) number of T's = 17,193,407 bp (32.16%) number of G's = 13,666,300 bp (25.56%) number of N's = 1,154 bp (0%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 261,019 number of insertions = 3,323 mapped reads with insertion percentage = 0.35% number of deletions = 8,224 mapped reads with deletion percentage = 0.88% homopolymer indels = 39.36% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 0.1614X There is a 1.61% of reference with a coverageData >= 1X There is a 0.09% 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 7729707 0.031011786325699866 0.2589611594865217 chr2 243199373 4425362 0.018196436715319987 0.17202305720974229 chr3 198022430 3473597 0.017541432048884562 0.13985494451396732 chr4 191154276 3350609 0.017528297405180724 0.14386872569957057 chr5 180915260 2603522 0.014390836903420972 0.12726859324329182 chr6 171115067 2759338 0.016125628493018677 0.13876407614992595 chr7 159138663 2204048 0.013849858723520883 0.14018580042526058 chr8 146364022 3354928 0.022921807929000476 0.17557481997465402 chr9 141213431 1927856 0.013652072514263888 0.15332528625676117 chr10 135534747 2518825 0.018584348705797192 0.1769985130353399 chr11 135006516 1680415 0.012446917747288583 0.14195222947087469 chr12 133851895 2358021 0.01761664263326268 0.14088891981479715 chr13 115169878 1633476 0.014183187725526635 0.12499839026960154 chr14 107349540 899904 0.008382932986950852 0.10249721057010126 chr15 102531392 1514333 0.014769457143427839 0.12831617843443016 chr16 90354753 1561912 0.017286439817947374 0.14623888012267533 chr17 81195210 1161187 0.014301176140809292 0.12812532290195996 chr18 78077248 1298517 0.016631183004810826 0.23830220658450543 chr19 59128983 981747 0.016603481916812268 0.19618689551353502 chr20 63025520 1605411 0.025472395943738346 0.17070018321552816 chr21 48129895 687797 0.01429043217318467 0.13206468063053362 chr22 51304566 631294 0.012304830724033412 0.11701035819337238 chrMT 16571 3714 0.2241264860298111 0.5221307264443179 chrX 155270560 2963072 0.019083282754953676 0.15570478041357075 chrY 59373566 152117 0.002562032403443647 0.06755770877069059