BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695973.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 14,026,800 number of mapped reads = 13,625,552 (97.14%) number of supplementary alignments = 43,376 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,904,625 number of mapped paired reads (second in pair) = 6,720,927 number of mapped paired reads (both in pair) = 13,381,280 number of mapped paired reads (singletons) = 244,272 number of mapped bases = 1,338,567,758 bp number of sequenced bases = 1,338,186,724 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 696,920 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 50,573.7571 std insert size = 2,149,831.7056 median insert size = 308 >>>>>>> Mapping quality mean mapping quality = 53.6327 >>>>>>> ACTG content number of A's = 394,630,349 bp (29.49%) number of C's = 274,207,916 bp (20.49%) number of T's = 393,049,002 bp (29.37%) number of G's = 276,188,549 bp (20.64%) number of N's = 110,908 bp (0.01%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 11,553,731 number of insertions = 135,112 mapped reads with insertion percentage = 0.96% number of deletions = 157,753 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.34% >>>>>>> Coverage mean coverageData = 0.4324X std coverageData = 4.9614X There is a 32.4% of reference with a coverageData >= 1X There is a 7.06% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 111052856 0.4455469581357633 11.174388838027962 chr2 243199373 117144436 0.48168066617507277 3.208991224570055 chr3 198022430 88354317 0.44618337932728125 0.8373167872812497 chr4 191154276 88060547 0.46067788198470644 3.358380742261161 chr5 180915260 80467330 0.4447791192406876 0.7845013751933082 chr6 171115067 77116521 0.45067054790680705 2.0060822242035403 chr7 159138663 72253157 0.4540264172007025 4.143562406135202 chr8 146364022 67102636 0.45846400695384004 3.0402193267352455 chr9 141213431 56354923 0.399076225263587 4.121235764416835 chr10 135534747 74458979 0.5493718817359802 13.061329003526362 chr11 135006516 61658906 0.45671059313907486 2.2690352490838417 chr12 133851895 59589003 0.4451860991583272 0.7757009382084507 chr13 115169878 41603862 0.36123909065875714 0.6732516950435539 chr14 107349540 40687698 0.3790207019051968 0.7338481309964902 chr15 102531392 38495250 0.37544842851640986 0.7128317975583046 chr16 90354753 42880507 0.47457942804624786 3.67339690979321 chr17 81195210 37955535 0.46746027259489814 2.116050814985763 chr18 78077248 36600694 0.4687754107316897 5.333172086193082 chr19 59128983 27155382 0.4592567066475674 5.97311416675206 chr20 63025520 28350363 0.44982354766767496 1.6743318528041662 chr21 48129895 18541560 0.38523998442132484 1.9653399389160844 chr22 51304566 17018914 0.3317231842483572 1.8970831608988046 chrMT 16571 3706445 223.67056906644137 42.519707878514026 chrX 155270560 35162238 0.22645785524313172 0.9844942333747881 chrY 59373566 16795699 0.2828817625675372 4.952664400343503