BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630890.sorted.bam outfile = SRP017516.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 = 53,111,368 number of mapped reads = 52,502,411 (98.85%) number of supplementary alignments = 304,762 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,455,918 number of mapped paired reads (second in pair) = 26,046,493 number of mapped paired reads (both in pair) = 52,056,134 number of mapped paired reads (singletons) = 446,277 number of mapped bases = 5,132,778,236 bp number of sequenced bases = 5,131,514,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,980,674 duplication rate = 17.3% >>>>>>> Insert size mean insert size = 394,955.6712 std insert size = 5,961,659.0269 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 50.9803 >>>>>>> ACTG content number of A's = 1,577,367,709 bp (30.74%) number of C's = 985,111,025 bp (19.2%) number of T's = 1,549,166,593 bp (30.19%) number of G's = 1,009,734,609 bp (19.68%) number of N's = 10,134,244 bp (0.2%) GC percentage = 38.87% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 57,817,702 number of insertions = 4,404,862 mapped reads with insertion percentage = 8.32% number of deletions = 649,611 mapped reads with deletion percentage = 1.21% homopolymer indels = 25.86% >>>>>>> Coverage mean coverageData = 1.658X std coverageData = 6.5316X There is a 26.47% of reference with a coverageData >= 1X There is a 18.42% of reference with a coverageData >= 2X There is a 13.63% of reference with a coverageData >= 3X There is a 10.81% of reference with a coverageData >= 4X There is a 8.85% of reference with a coverageData >= 5X There is a 7.44% of reference with a coverageData >= 6X There is a 6.38% of reference with a coverageData >= 7X There is a 5.54% of reference with a coverageData >= 8X There is a 4.87% of reference with a coverageData >= 9X There is a 4.32% of reference with a coverageData >= 10X There is a 3.86% of reference with a coverageData >= 11X There is a 3.48% of reference with a coverageData >= 12X There is a 3.15% of reference with a coverageData >= 13X There is a 2.87% of reference with a coverageData >= 14X There is a 2.62% of reference with a coverageData >= 15X There is a 2.4% of reference with a coverageData >= 16X There is a 2.21% of reference with a coverageData >= 17X There is a 2.04% of reference with a coverageData >= 18X There is a 1.89% of reference with a coverageData >= 19X There is a 1.75% of reference with a coverageData >= 20X There is a 1.63% of reference with a coverageData >= 21X There is a 1.52% of reference with a coverageData >= 22X There is a 1.42% of reference with a coverageData >= 23X There is a 1.33% of reference with a coverageData >= 24X There is a 1.24% of reference with a coverageData >= 25X There is a 1.17% of reference with a coverageData >= 26X There is a 1.1% of reference with a coverageData >= 27X There is a 1.03% of reference with a coverageData >= 28X There is a 0.97% of reference with a coverageData >= 29X There is a 0.91% of reference with a coverageData >= 30X There is a 0.86% of reference with a coverageData >= 31X There is a 0.82% of reference with a coverageData >= 32X There is a 0.77% of reference with a coverageData >= 33X There is a 0.73% of reference with a coverageData >= 34X There is a 0.69% of reference with a coverageData >= 35X There is a 0.66% of reference with a coverageData >= 36X There is a 0.62% of reference with a coverageData >= 37X There is a 0.59% of reference with a coverageData >= 38X There is a 0.56% of reference with a coverageData >= 39X There is a 0.53% of reference with a coverageData >= 40X There is a 0.51% of reference with a coverageData >= 41X There is a 0.48% of reference with a coverageData >= 42X There is a 0.46% of reference with a coverageData >= 43X There is a 0.44% of reference with a coverageData >= 44X There is a 0.42% of reference with a coverageData >= 45X There is a 0.4% of reference with a coverageData >= 46X There is a 0.38% of reference with a coverageData >= 47X There is a 0.37% of reference with a coverageData >= 48X There is a 0.35% of reference with a coverageData >= 49X There is a 0.33% of reference with a coverageData >= 50X There is a 0.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 417581055 1.6753460967304872 6.763439033231623 chr2 243199373 483342540 1.987433331088399 7.107257225427278 chr3 198022430 434639821 2.194901966408553 7.458439118795364 chr4 191154276 439674856 2.3001047384365076 8.308901253841967 chr5 180915260 385498336 2.130822662499559 7.305217959594921 chr6 171115067 347879965 2.0330177295258283 7.398456432091616 chr7 159138663 296767220 1.864834191801649 7.413535460914908 chr8 146364022 319075974 2.180016438739296 8.184118609939969 chr9 141213431 223573730 1.5832327592125426 6.483849695608396 chr10 135534747 248201858 1.8312784248603053 7.635132582061622 chr11 135006516 262993963 1.9480094057089807 6.85437514851884 chr12 133851895 224818742 1.679608211747768 6.191079472530573 chr13 115169878 169429279 1.4711249325105649 5.213126516801588 chr14 107349540 169651873 1.5803688865364491 6.123983069372444 chr15 102531392 122753683 1.1972302394958219 4.419439754955849 chr16 90354753 106073009 1.173961584511221 4.64313817534658 chr17 81195210 82441253 1.0153462624211453 4.369460813562963 chr18 78077248 141266103 1.809312016222703 5.718425996511763 chr19 59128983 29704599 0.5023695232505521 2.0886212939321385 chr20 63025520 74620879 1.1839787914482895 5.069441346564737 chr21 48129895 69280191 1.439441972603514 6.0774758404829505 chr22 51304566 26263517 0.5119138323867705 2.2132154766540943 chrMT 16571 3036 0.1832116347836582 0.8939266990977157 chrX 155270560 8090533 0.052106033494050644 0.8575546280040802 chrY 59373566 49152221 0.8278468738091291 4.263696389927223