BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008720.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,491,839 number of mapped reads = 1,208,401 (81%) number of supplementary alignments = 5,752 (0.39%) number of secondary alignments = 0 number of mapped bases = 84,296,738 bp number of sequenced bases = 84,255,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,836 duplication rate = 1.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4764 >>>>>>> ACTG content number of A's = 28,024,747 bp (33.26%) number of C's = 14,253,167 bp (16.92%) number of T's = 24,675,058 bp (29.29%) number of G's = 17,297,738 bp (20.53%) number of N's = 4,732 bp (0.01%) GC percentage = 37.45% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 703,750 number of insertions = 6,414 mapped reads with insertion percentage = 0.53% number of deletions = 26,306 mapped reads with deletion percentage = 2.15% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.206X There is a 2.44% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5761661 0.023115934383168498 0.24281807449417178 chr2 243199373 8245003 0.03390223789762813 0.2659046283937258 chr3 198022430 8647137 0.04366746231727386 0.22876104468131983 chr4 191154276 1827970 0.0095627994217613 0.10597265163549387 chr5 180915260 3956055 0.021866895031408626 0.1601797982264742 chr6 171115067 3873731 0.022638164294439368 0.17091281629141244 chr7 159138663 5895840 0.03704844497782415 0.2565952890323172 chr8 146364022 11374862 0.0777162436817977 0.35885260753480225 chr9 141213431 3156756 0.02235450252603805 0.16874028377028416 chr10 135534747 3536237 0.02609099938040243 0.19714807939273002 chr11 135006516 2921793 0.021641866530353247 0.17543141729617684 chr12 133851895 3314238 0.024760486207535574 0.17098322029857654 chr13 115169878 989020 0.008587488475068107 0.0996371600575824 chr14 107349540 3230492 0.030093207665351895 0.1913977839719238 chr15 102531392 2472302 0.0241126346943578 0.17192648991665904 chr16 90354753 1945186 0.021528319600408845 0.16309072005853073 chr17 81195210 2586409 0.03185420667056591 0.2041612606856353 chr18 78077248 1450099 0.01857261926035098 0.23521725188942316 chr19 59128983 1507211 0.025490223635336328 0.1917139644367275 chr20 63025520 739703 0.01173656322073979 0.117149316257218 chr21 48129895 822690 0.017093118528515385 0.14531368920625473 chr22 51304566 899294 0.017528537323559076 0.14351332022747226 chrMT 16571 17667 1.0661396415424538 1.321735610135952 chrX 155270560 4996570 0.03217976414846446 0.2033002274508138 chrY 59373566 128812 0.0021695176604349486 0.053551745698458345