BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124883.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,585,196 number of mapped reads = 3,553,936 (99.13%) number of supplementary alignments = 45,902 (1.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,784,217 number of mapped paired reads (second in pair) = 1,769,719 number of mapped paired reads (both in pair) = 3,537,240 number of mapped paired reads (singletons) = 16,696 number of mapped bases = 509,775,784 bp number of sequenced bases = 509,474,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 461,429 duplication rate = 10.8% >>>>>>> Insert size mean insert size = 97,843.4635 std insert size = 3,020,549.2555 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 53.7849 >>>>>>> ACTG content number of A's = 148,204,757 bp (29.09%) number of C's = 105,254,958 bp (20.66%) number of T's = 146,666,608 bp (28.79%) number of G's = 109,301,403 bp (21.45%) number of N's = 47,198 bp (0.01%) GC percentage = 42.11% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 4,165,068 number of insertions = 70,465 mapped reads with insertion percentage = 1.89% number of deletions = 150,744 mapped reads with deletion percentage = 4.1% homopolymer indels = 49.15% >>>>>>> Coverage mean coverageData = 0.1647X std coverageData = 2.4027X There is a 8.59% of reference with a coverageData >= 1X There is a 4.73% of reference with a coverageData >= 2X There is a 1.25% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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% 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 44058861 0.1767653008174451 1.1690479013634838 chr2 243199373 39275156 0.16149365648241207 1.3191063200084412 chr3 198022430 40242308 0.2032209583530512 0.7776450090645758 chr4 191154276 29492099 0.1542842755973714 0.9023997758516826 chr5 180915260 34911699 0.19297266023883225 0.6746393958109475 chr6 171115067 23402559 0.13676504010018006 0.7095117944982464 chr7 159138663 34622194 0.21755991502831715 1.6076508338214268 chr8 146364022 26449885 0.18071302386046756 0.6974634597064324 chr9 141213431 18777836 0.13297485846087828 1.6625054997710216 chr10 135534747 27042872 0.19952722529522263 8.827488593661927 chr11 135006516 21752151 0.16111926775445418 1.4997852929863622 chr12 133851895 30720832 0.22951361278822388 0.7472522986183279 chr13 115169878 11372941 0.09874926671364538 0.45993944243964485 chr14 107349540 11813943 0.11005117488160639 0.5007707223505273 chr15 102531392 11619960 0.1133307543508236 0.49147970910078337 chr16 90354753 20659842 0.22865252036049505 6.609889580581839 chr17 81195210 13250526 0.1631934445394008 1.4383540602481681 chr18 78077248 8649016 0.1107751133851439 1.8902032689536632 chr19 59128983 5880328 0.09944916522579121 0.7578202691583388 chr20 63025520 10422483 0.16536925042427258 0.6606471641531888 chr21 48129895 5240766 0.10888795830533185 0.6573379740180281 chr22 51304566 3513092 0.06847523084007766 0.3945709122595086 chrMT 16571 221650 13.37577695974896 8.430089975775797 chrX 155270560 31756498 0.2045236263719278 1.0764598746045735 chrY 59373566 4626287 0.07791829448141956 1.3028285748981172