BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231782.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 = 4,612,720 number of mapped reads = 4,109,963 (89.1%) number of supplementary alignments = 29,930 (0.65%) number of secondary alignments = 0 number of mapped bases = 268,624,701 bp number of sequenced bases = 268,516,745 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 274,948 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9491 >>>>>>> ACTG content number of A's = 77,289,038 bp (28.78%) number of C's = 52,063,475 bp (19.39%) number of T's = 73,759,833 bp (27.47%) number of G's = 65,385,722 bp (24.35%) number of N's = 18,677 bp (0.01%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,808,717 number of insertions = 19,658 mapped reads with insertion percentage = 0.47% number of deletions = 64,123 mapped reads with deletion percentage = 1.54% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.0868X std coverageData = 16.9627X There is a 7.04% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 26661000 0.10696462818441684 2.0249161343250215 chr2 243199373 26597812 0.10936628524942785 60.452768225014175 chr3 198022430 26783787 0.13525632929562575 0.4187016983046826 chr4 191154276 9058986 0.04739096707415533 0.2798934128936797 chr5 180915260 10751516 0.05942846391177836 0.2909553475573865 chr6 171115067 21347757 0.1247567346012844 0.6583168853914911 chr7 159138663 14426210 0.09065182356094069 1.0149811863615001 chr8 146364022 16091082 0.10993877990043209 0.9862737565807366 chr9 141213431 12223786 0.08656248852136451 0.5936050264378853 chr10 135534747 10964649 0.08089917340532608 0.6513364453130465 chr11 135006516 9022859 0.06683276679771516 0.5671720946981429 chr12 133851895 9908568 0.07402635577180286 0.3181135504729448 chr13 115169878 7244534 0.0629030274739025 0.2811220474716094 chr14 107349540 11554594 0.10763524464101104 0.5595729994606594 chr15 102531392 4590113 0.044767879480266885 0.24801468021129866 chr16 90354753 7162345 0.07926915587938135 0.4129438149566672 chr17 81195210 6878533 0.08471599494600729 0.4408454392107828 chr18 78077248 4000338 0.051235642936595306 1.2294169256219571 chr19 59128983 7292024 0.12332402199442531 1.1581304261941832 chr20 63025520 6748972 0.10708316250306225 0.39801435998814666 chr21 48129895 4050621 0.08416018775856461 0.3614552762778406 chr22 51304566 2846269 0.05547788865419893 0.2664822795784233 chrMT 16571 109971 6.636352664293042 4.291129357632585 chrX 155270560 11743745 0.07563407383859504 0.3833471284270115 chrY 59373566 564630 0.00950978757112214 0.1767494646253753