BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081021.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,885,961 number of mapped reads = 2,069,214 (71.7%) number of supplementary alignments = 11,735 (0.41%) number of secondary alignments = 0 number of mapped bases = 125,935,139 bp number of sequenced bases = 125,893,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,857 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0577 >>>>>>> ACTG content number of A's = 36,270,386 bp (28.81%) number of C's = 25,347,290 bp (20.13%) number of T's = 36,617,395 bp (29.09%) number of G's = 27,656,593 bp (21.97%) number of N's = 1,738 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 900,718 number of insertions = 8,472 mapped reads with insertion percentage = 0.41% number of deletions = 24,138 mapped reads with deletion percentage = 1.16% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.2982X There is a 3.44% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 10898307 0.043724292265654975 0.4494120221444076 chr2 243199373 10767251 0.04427335016196773 0.3144570161262653 chr3 198022430 8088954 0.04084867557680208 0.23216501400618736 chr4 191154276 9012563 0.04714811087982149 0.26067394486069956 chr5 180915260 7176673 0.03966869903622282 0.22895407543748714 chr6 171115067 7435851 0.04345526744293067 0.26710200858181427 chr7 159138663 6506334 0.040884684320868024 0.4092907238403887 chr8 146364022 5477616 0.03742460698435849 0.3053205180505274 chr9 141213431 4846874 0.03432303829513214 0.26799710639476 chr10 135534747 6645583 0.04903231936530637 0.29493311141880885 chr11 135006516 5414699 0.04010694565290463 0.2793993624554155 chr12 133851895 6286766 0.046968076171054585 0.25270285695467487 chr13 115169878 3570655 0.03100337572642041 0.201241252191006 chr14 107349540 3887636 0.03621474297887071 0.22805622790603472 chr15 102531392 3801638 0.03707779564721017 0.22872486200233036 chr16 90354753 3285472 0.03636191667747683 0.23859720355552244 chr17 81195210 3272744 0.04030710678622544 0.24702096799510453 chr18 78077248 3222433 0.04127236912858404 0.5022202851607144 chr19 59128983 2312682 0.03911249412153766 0.3451324084098612 chr20 63025520 2805805 0.04451855375409834 0.2466666566158383 chr21 48129895 1723227 0.035803672540735854 0.23049026142013898 chr22 51304566 1386423 0.02702338423445586 0.1882422557896763 chrMT 16571 64774 3.90887695371432 2.906228648340553 chrX 155270560 7684812 0.04949303976233486 0.2781563743025594 chrY 59373566 359367 0.006052643022991073 0.12486553162750573