BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717033.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 484,922 number of mapped reads = 411,680 (84.9%) number of supplementary alignments = 1,751 (0.36%) number of secondary alignments = 0 number of mapped bases = 23,227,875 bp number of sequenced bases = 23,221,078 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,642 duplication rate = 1.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9209 >>>>>>> ACTG content number of A's = 5,514,152 bp (23.75%) number of C's = 4,264,312 bp (18.36%) number of T's = 7,511,709 bp (32.35%) number of G's = 5,930,631 bp (25.54%) number of N's = 274 bp (0%) GC percentage = 43.9% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 121,613 number of insertions = 1,770 mapped reads with insertion percentage = 0.43% number of deletions = 4,265 mapped reads with deletion percentage = 1.03% homopolymer indels = 38.84% >>>>>>> Coverage mean coverageData = 0.0075X std coverageData = 0.1005X There is a 0.72% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 1989374 0.007981420435458013 0.12707435932905237 chr2 243199373 2323203 0.00955266854244727 0.13661840453082988 chr3 198022430 1625119 0.008206742034223093 0.09334239965551788 chr4 191154276 1268386 0.00663540479732716 0.08574922669382747 chr5 180915260 1322000 0.007307288506232144 0.08780470057497897 chr6 171115067 1289919 0.007538313385343209 0.09233505600650982 chr7 159138663 1157576 0.00727400857954927 0.11951682417555327 chr8 146364022 1646903 0.011252102651292268 0.11505723920053001 chr9 141213431 1018148 0.007209994069190203 0.09124942232072386 chr10 135534747 1129880 0.008336460022314425 0.11067352062594138 chr11 135006516 797136 0.005904426124143519 0.08304773191189446 chr12 133851895 1001211 0.007479991224629281 0.08936290430604102 chr13 115169878 616252 0.00535080882867654 0.07486349885717941 chr14 107349540 759457 0.00707461811201054 0.08709211322980111 chr15 102531392 571992 0.005578701204017595 0.0766573899153446 chr16 90354753 688562 0.007620650570535011 0.09139932258099209 chr17 81195210 1017565 0.012532327953828803 0.11724780925983239 chr18 78077248 516093 0.006610030619931686 0.09855226775914634 chr19 59128983 484880 0.00820037780795249 0.11094360392186138 chr20 63025520 530494 0.008417130076832369 0.0943966430436949 chr21 48129895 244395 0.0050778211753838235 0.07383124199990397 chr22 51304566 321791 0.006272170784955086 0.08167289417132549 chrMT 16571 3434 0.20722949731458573 0.47327901058302596 chrX 155270560 850267 0.005476034864561575 0.07994637020643858 chrY 59373566 53838 9.067671630166192E-4 0.03419127450739192