BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240262.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 = 1,471,727 number of mapped reads = 1,207,186 (82.03%) number of supplementary alignments = 6,059 (0.41%) number of secondary alignments = 0 number of mapped bases = 74,476,690 bp number of sequenced bases = 74,433,424 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,090 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.3235 >>>>>>> ACTG content number of A's = 20,053,826 bp (26.94%) number of C's = 13,184,563 bp (17.71%) number of T's = 23,067,428 bp (30.99%) number of G's = 18,110,413 bp (24.33%) number of N's = 17,194 bp (0.02%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 752,110 number of insertions = 6,044 mapped reads with insertion percentage = 0.5% number of deletions = 24,842 mapped reads with deletion percentage = 2.03% homopolymer indels = 48.3% >>>>>>> Coverage mean coverageData = 0.0241X std coverageData = 0.2556X There is a 2.11% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 5004640 0.020078746363484487 0.3633367213651354 chr2 243199373 8304885 0.034148463861376814 0.3443959164423065 chr3 198022430 4740978 0.02394162115877479 0.17394294262084412 chr4 191154276 4212493 0.022037137165584513 0.17072058316192792 chr5 180915260 3615282 0.01998328941406048 0.16098181694025362 chr6 171115067 3870016 0.022616453757400568 0.20744444713952437 chr7 159138663 4271215 0.026839580774912 0.4130620764498876 chr8 146364022 4082833 0.027895058800720848 0.30977156213023216 chr9 141213431 2571540 0.018210307488386143 0.2437497040169186 chr10 135534747 3417451 0.02521457468024786 0.22637296889350556 chr11 135006516 3305760 0.024485929256925644 0.2485223812184365 chr12 133851895 3559724 0.026594498344606924 0.1824508318811277 chr13 115169878 1384462 0.012021042515995372 0.12249244159346521 chr14 107349540 3056536 0.028472744270725332 0.20249564600432993 chr15 102531392 1822494 0.017774985440556584 0.16626463353015825 chr16 90354753 3143521 0.03479087591551493 0.21798460927736926 chr17 81195210 2547370 0.031373402445784675 0.2144801696575785 chr18 78077248 1469562 0.018821898025914028 0.40822546768684276 chr19 59128983 1974011 0.03338482923002413 0.3008694161526006 chr20 63025520 1786842 0.028351086988254916 0.19206999500452226 chr21 48129895 1331468 0.02766405370300517 0.194009556353583 chr22 51304566 962982 0.018769908315762772 0.1517331446794825 chrMT 16571 30637 1.8488322973870013 2.1832804328858355 chrX 155270560 3830408 0.024669248310819514 0.200580163094139 chrY 59373566 179580 0.0030245783114997674 0.07263440214050741