BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124884.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,579,268 number of mapped reads = 5,421,286 (97.17%) number of supplementary alignments = 5,559 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,757,142 number of mapped paired reads (second in pair) = 2,664,144 number of mapped paired reads (both in pair) = 5,315,040 number of mapped paired reads (singletons) = 106,246 number of mapped bases = 339,221,883 bp number of sequenced bases = 339,093,654 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 273,383 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 27,840.4383 std insert size = 1,598,669.9285 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 51.9415 >>>>>>> ACTG content number of A's = 92,635,597 bp (27.32%) number of C's = 61,424,327 bp (18.11%) number of T's = 100,880,202 bp (29.75%) number of G's = 84,150,821 bp (24.82%) number of N's = 2,707 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 2,073,935 number of insertions = 33,044 mapped reads with insertion percentage = 0.6% number of deletions = 87,287 mapped reads with deletion percentage = 1.59% homopolymer indels = 50% >>>>>>> Coverage mean coverageData = 0.1096X std coverageData = 0.7025X There is a 8.64% of reference with a coverageData >= 1X There is a 1.54% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 30500647 0.12236939221106294 0.9672984120273374 chr2 243199373 29212773 0.12011861971371118 0.7650308180380868 chr3 198022430 21525050 0.10870005988715521 0.38850621648709227 chr4 191154276 15016051 0.07855461731863116 0.3793026831868948 chr5 180915260 17755585 0.09814310301961261 0.3659275661779992 chr6 171115067 20444665 0.11947904622566054 0.6529994745154242 chr7 159138663 22356205 0.14048254885740746 1.0934495448480344 chr8 146364022 19120582 0.130637172569636 0.5186876120099452 chr9 141213431 14134863 0.10009574089308827 0.6084868123243224 chr10 135534747 14637847 0.10800069593961761 1.3426370815644004 chr11 135006516 22229609 0.16465582298264775 0.6496533937287589 chr12 133851895 11571651 0.08645115558505914 0.34366803272799645 chr13 115169878 15627836 0.1356937792362687 0.5676511940686845 chr14 107349540 5703676 0.05313181593512185 0.30379084295840586 chr15 102531392 7610113 0.07422227331118258 0.33255706577301897 chr16 90354753 9814216 0.10861870210635184 1.0799019367753635 chr17 81195210 8347773 0.10281115105189087 0.6884243173828216 chr18 78077248 8961412 0.11477622776868365 0.9861557921522383 chr19 59128983 6308297 0.10668705396133737 0.7978049892966123 chr20 63025520 9613181 0.1525283885004043 0.473744808572324 chr21 48129895 2813517 0.05845674502302571 0.2993755004125139 chr22 51304566 2891237 0.056354379842137245 0.2732984778780848 chrMT 16571 44890 2.7089493693802424 2.7897002515897316 chrX 155270560 22497541 0.1448925089212018 0.5782204541273304 chrY 59373566 482666 0.008129307914569254 0.3098541758514954