BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975221.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 3,773,288 number of mapped reads = 3,729,776 (98.85%) number of supplementary alignments = 14,165 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,864,320 number of mapped paired reads (second in pair) = 1,865,456 number of mapped paired reads (both in pair) = 3,717,734 number of mapped paired reads (singletons) = 12,042 number of mapped bases = 340,039,344 bp number of sequenced bases = 339,839,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,757 duplication rate = 2.23% >>>>>>> Insert size mean insert size = 57,139.0134 std insert size = 2,339,536.5132 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 53 >>>>>>> ACTG content number of A's = 100,021,072 bp (29.43%) number of C's = 66,981,026 bp (19.71%) number of T's = 100,033,058 bp (29.44%) number of G's = 72,799,795 bp (21.42%) number of N's = 4,676 bp (0%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,870,311 number of insertions = 58,343 mapped reads with insertion percentage = 1.53% number of deletions = 122,093 mapped reads with deletion percentage = 3.2% homopolymer indels = 46.77% >>>>>>> Coverage mean coverageData = 0.1098X std coverageData = 0.9807X There is a 7.9% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% 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% 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 39799530 0.15967675362381545 1.1345309307631803 chr2 243199373 26244979 0.10791548792356467 0.9727825103514635 chr3 198022430 22690390 0.1145849487858522 0.43927125041738824 chr4 191154276 17453609 0.09130640111864409 0.6383614500705563 chr5 180915260 18656843 0.10312476128326599 0.40102004945629127 chr6 171115067 22140960 0.12939222938211514 0.5941044120706521 chr7 159138663 19906526 0.1250891871574917 1.0742548561591916 chr8 146364022 21209865 0.1449117393070819 0.5407350289206048 chr9 141213431 12049872 0.08533092011623172 0.8663770174710688 chr10 135534747 12884246 0.09506230900331411 2.9275653675587137 chr11 135006516 15475526 0.11462799321478676 0.7948094034781921 chr12 133851895 18676080 0.1395279461676654 0.4727018167040421 chr13 115169878 5888574 0.05112946286180836 0.2732674162797885 chr14 107349540 8602091 0.0801316055942112 0.3664811969881075 chr15 102531392 5814724 0.05671164593181374 0.2902820816977679 chr16 90354753 9602619 0.10627685518657773 1.627721655959699 chr17 81195210 10563307 0.13009766216504642 1.1355898054952434 chr18 78077248 10412496 0.13336146274008018 1.0387465740190147 chr19 59128983 8456138 0.14301172742984603 0.73461189666425 chr20 63025520 8221607 0.1304488562728241 0.47086052885474433 chr21 48129895 5683557 0.1180878744904804 0.5058435022654113 chr22 51304566 2132380 0.0415631622339423 0.26320608011158053 chrMT 16571 35333 2.132218936696639 2.071808715579209 chrX 155270560 14483335 0.09327804961867851 0.4839802052430174 chrY 59373566 2954757 0.049765530337187426 0.9220584321126801