BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238513.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 = 1,706,112 number of mapped reads = 1,299,448 (76.16%) number of supplementary alignments = 8,512 (0.5%) number of secondary alignments = 0 number of mapped bases = 79,228,574 bp number of sequenced bases = 79,188,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 494,514 duplication rate = 22.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0025 >>>>>>> ACTG content number of A's = 19,018,550 bp (24.02%) number of C's = 13,480,223 bp (17.02%) number of T's = 27,430,795 bp (34.64%) number of G's = 19,253,955 bp (24.31%) number of N's = 4,937 bp (0.01%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 507,288 number of insertions = 5,679 mapped reads with insertion percentage = 0.43% number of deletions = 24,225 mapped reads with deletion percentage = 1.84% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.0256X std coverageData = 0.5936X There is a 0.88% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 6945681 0.027866253540848752 0.468027244286029 chr2 243199373 6768362 0.02783050760579058 1.4031755095628562 chr3 198022430 5113098 0.025820802219223348 0.42086542652917114 chr4 191154276 5037708 0.02635414757868142 0.40395922306759174 chr5 180915260 4507373 0.024914277546294324 0.3957322065528507 chr6 171115067 5117785 0.029908441668669655 0.6088755806558264 chr7 159138663 4521970 0.028415282086415417 0.4996117531059131 chr8 146364022 4496652 0.030722386133936658 0.4899654996977541 chr9 141213431 3265969 0.023127892133716375 0.4022642662360991 chr10 135534747 3566735 0.026316019168132584 0.4127218159898233 chr11 135006516 3518507 0.026061756900681743 0.42506086643429597 chr12 133851895 3647445 0.027249857015472213 0.4330262020129366 chr13 115169878 2257744 0.019603598086645538 0.45232789501640464 chr14 107349540 2211479 0.02060073103247578 0.3639096656396604 chr15 102531392 1987965 0.019388842394727265 0.4104429853537179 chr16 90354753 2238898 0.024778973165916353 0.41432797039858865 chr17 81195210 1934544 0.023825838987299865 0.3905665632502386 chr18 78077248 2067943 0.026485859235202552 1.0054130539254669 chr19 59128983 1631085 0.027585203012877795 0.4481147438715228 chr20 63025520 1817798 0.028842253106360724 0.4189283724366885 chr21 48129895 1152914 0.023954218059274803 0.40467314455715697 chr22 51304566 933394 0.01819319551402111 0.35168292869525586 chrMT 16571 13747 0.8295817995292982 1.8651681024814042 chrX 155270560 4208148 0.02710203402370675 0.4163168289515524 chrY 59373566 265630 0.004473876472233452 0.21977821215363805