BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240023.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 = 1,435,313 number of mapped reads = 1,148,331 (80.01%) number of supplementary alignments = 3,976 (0.28%) number of secondary alignments = 0 number of mapped bases = 70,948,819 bp number of sequenced bases = 70,909,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,303 duplication rate = 4.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9946 >>>>>>> ACTG content number of A's = 18,927,727 bp (26.69%) number of C's = 12,030,339 bp (16.97%) number of T's = 23,335,625 bp (32.91%) number of G's = 16,569,613 bp (23.37%) number of N's = 46,245 bp (0.07%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 685,819 number of insertions = 4,911 mapped reads with insertion percentage = 0.43% number of deletions = 22,438 mapped reads with deletion percentage = 1.93% homopolymer indels = 49.86% >>>>>>> Coverage mean coverageData = 0.0229X std coverageData = 0.2288X There is a 1.91% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.05% 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 5736261 0.0230140289199119 0.3002498844805659 chr2 243199373 8983648 0.036939437339750046 0.2967821290738242 chr3 198022430 4644520 0.023454514723407847 0.17955643467078197 chr4 191154276 4772199 0.024965170017959733 0.19080507512995748 chr5 180915260 3162103 0.01747836528549333 0.1554314011759836 chr6 171115067 3213772 0.018781350212719726 0.18018770416579868 chr7 159138663 4326771 0.02718868512801317 0.40737252824314774 chr8 146364022 4154697 0.028386053780347743 0.2775271941872267 chr9 141213431 2441930 0.017292476945765873 0.19697260247870754 chr10 135534747 3313829 0.02445003272850762 0.20768251057162693 chr11 135006516 3015024 0.02233243319900204 0.22318185562735643 chr12 133851895 3776449 0.02821363866383812 0.19883301447911833 chr13 115169878 1368086 0.011878852558999845 0.12768414908666428 chr14 107349540 2523637 0.023508596310706127 0.183496762221547 chr15 102531392 2128314 0.020757681705911104 0.18146443967476067 chr16 90354753 2079745 0.023017549502902187 0.1798333723046506 chr17 81195210 1488185 0.018328482677734313 0.1696850038407803 chr18 78077248 1461424 0.01871766791780366 0.28052963589928187 chr19 59128983 1234110 0.02087149038230541 0.2270709804713884 chr20 63025520 1313305 0.0208376702008964 0.1701868805475211 chr21 48129895 1269218 0.026370678764206738 0.19430336725540256 chr22 51304566 544786 0.010618665013168613 0.11794934940229299 chrMT 16571 17179 1.0366906040673465 1.4558926430168515 chrX 155270560 3836841 0.024710679216974552 0.19387338627807552 chrY 59373566 142786 0.00240487492363184 0.05942942735968931