BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013356.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 = 1,534,910 number of mapped reads = 970,489 (63.23%) number of supplementary alignments = 5,577 (0.36%) number of secondary alignments = 0 number of mapped bases = 57,572,157 bp number of sequenced bases = 57,546,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,578 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1343 >>>>>>> ACTG content number of A's = 16,805,235 bp (29.2%) number of C's = 11,123,360 bp (19.33%) number of T's = 17,137,179 bp (29.78%) number of G's = 12,479,685 bp (21.69%) number of N's = 696 bp (0%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 447,332 number of insertions = 4,129 mapped reads with insertion percentage = 0.42% number of deletions = 15,118 mapped reads with deletion percentage = 1.54% homopolymer indels = 43.77% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.2016X There is a 1.64% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 5400899 0.02166854781878357 0.31516831226815334 chr2 243199373 4435387 0.01823765803869897 0.2368121456676876 chr3 198022430 2996076 0.015129983002430583 0.13774063337917328 chr4 191154276 3136273 0.016407025077482443 0.15657380462446183 chr5 180915260 4506999 0.024912210280105724 0.17475396015989436 chr6 171115067 1145547 0.0066946004234682615 0.10085917137486254 chr7 159138663 3696824 0.023230206477227976 0.2729037354315685 chr8 146364022 3359980 0.022956324608242866 0.24578507284970097 chr9 141213431 3236241 0.0229173739146668 0.19803196913109006 chr10 135534747 2987312 0.02204093095034884 0.24712965700451467 chr11 135006516 2993464 0.02217273720329173 0.1809279836157562 chr12 133851895 3221941 0.024070940497331023 0.1738658152727416 chr13 115169878 1499251 0.013017735418630903 0.1273191810822478 chr14 107349540 1305490 0.012161114057871137 0.1301582311082218 chr15 102531392 1149498 0.01121118105955296 0.11784954256905236 chr16 90354753 1686066 0.018660512524449047 0.16221425741598247 chr17 81195210 1649743 0.020318230595129935 0.17012465921601086 chr18 78077248 1821246 0.02332620637448697 0.2916997458303353 chr19 59128983 1215221 0.020552036215471522 0.23947154157174855 chr20 63025520 1167333 0.0185215925231557 0.1521049332601547 chr21 48129895 729928 0.015165792487184939 0.14939815672034373 chr22 51304566 610538 0.011900266342765671 0.12035539109428858 chrMT 16571 18275 1.1028302456098003 1.4111896796516274 chrX 155270560 3428948 0.02208369699961152 0.17870541871129955 chrY 59373566 173677 0.002925156962948798 0.09102539389807073