BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231750.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 = 6,232,223 number of mapped reads = 5,899,015 (94.65%) number of supplementary alignments = 28,447 (0.46%) number of secondary alignments = 0 number of mapped bases = 400,136,579 bp number of sequenced bases = 399,994,591 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 500,910 duplication rate = 3.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6847 >>>>>>> ACTG content number of A's = 103,331,759 bp (25.83%) number of C's = 77,005,980 bp (19.25%) number of T's = 113,566,604 bp (28.39%) number of G's = 106,000,860 bp (26.5%) number of N's = 89,388 bp (0.02%) GC percentage = 45.75% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,630,572 number of insertions = 28,554 mapped reads with insertion percentage = 0.48% number of deletions = 86,501 mapped reads with deletion percentage = 1.45% homopolymer indels = 46.34% >>>>>>> Coverage mean coverageData = 0.1293X std coverageData = 29.8719X There is a 8.74% of reference with a coverageData >= 1X There is a 2.24% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 46779812 0.18768182728018157 1.4969121908666039 chr2 243199373 38373585 0.15778652932629067 106.51986207372283 chr3 198022430 20506931 0.10355862717167949 0.4235990042754921 chr4 191154276 11126819 0.05820858017322092 0.4158078349902405 chr5 180915260 18692268 0.10332057118896439 0.4370063421211578 chr6 171115067 38675620 0.22602112530511412 1.1298746003259548 chr7 159138663 27051999 0.16999011107690404 2.4413159391146415 chr8 146364022 23476890 0.16040068918029596 0.7978826067324903 chr9 141213431 8748765 0.06195419896001252 0.78259912572908 chr10 135534747 18657171 0.13765599901846573 0.7178008805610696 chr11 135006516 13736364 0.10174593350738716 1.068539068479634 chr12 133851895 13520823 0.10101331027102754 0.42320989951015536 chr13 115169878 15379270 0.1335355239327422 0.4918488830745232 chr14 107349540 14370354 0.1338650729197349 0.7321256999144712 chr15 102531392 6091505 0.059411121620196086 0.33919941193245395 chr16 90354753 10436340 0.11550405101544575 0.5829001810897187 chr17 81195210 10822645 0.13329166831393133 0.6609413421945527 chr18 78077248 3917944 0.05018035471742037 1.9315409632693552 chr19 59128983 12948576 0.2189886472425883 1.118250846385417 chr20 63025520 6949447 0.11026401686174109 0.4879161170403531 chr21 48129895 9293521 0.193092484411196 0.6836937551530903 chr22 51304566 8007140 0.15607070918405197 0.5712825248186514 chrMT 16571 16459 0.9932412045139098 1.4416438309806032 chrX 155270560 21556578 0.13883235817530382 0.6953677659110646 chrY 59373566 999753 0.016838351935944018 0.26082764326401986