BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777302.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,806,594 number of mapped reads = 1,755,048 (97.15%) number of supplementary alignments = 69,329 (3.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 879,911 number of mapped paired reads (second in pair) = 875,137 number of mapped paired reads (both in pair) = 1,745,376 number of mapped paired reads (singletons) = 9,672 number of mapped bases = 167,930,893 bp number of sequenced bases = 167,860,793 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,985 duplication rate = 8.86% >>>>>>> Insert size mean insert size = 177,868.7996 std insert size = 4,068,472.3293 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.8415 >>>>>>> ACTG content number of A's = 49,546,114 bp (29.52%) number of C's = 34,488,979 bp (20.55%) number of T's = 48,546,738 bp (28.92%) number of G's = 35,276,257 bp (21.02%) number of N's = 2,705 bp (0%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,057,663 number of insertions = 39,043 mapped reads with insertion percentage = 2.16% number of deletions = 25,075 mapped reads with deletion percentage = 1.37% homopolymer indels = 42.25% >>>>>>> Coverage mean coverageData = 0.0542X std coverageData = 0.8882X There is a 3.67% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% 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 0.01% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 13678386 0.054878041808369256 1.5257065894327617 chr2 243199373 14964929 0.06153358380574443 0.6682654488417588 chr3 198022430 11308438 0.057106854006387056 0.3827146927089531 chr4 191154276 11619283 0.060784844802530075 0.737414916036574 chr5 180915260 10336430 0.05713409692471492 0.3088559150971003 chr6 171115067 9795441 0.0572447603342843 0.38365747701175523 chr7 159138663 6608056 0.04152388788135037 0.6457094080525893 chr8 146364022 8543180 0.05836939900435368 0.4623919388529614 chr9 141213431 7090779 0.05021320528640084 0.7072769838026249 chr10 135534747 9599365 0.07082585988078761 2.0925798237295714 chr11 135006516 7709534 0.05710490299594132 0.3932116948255927 chr12 133851895 7528568 0.05624550926230817 0.3036362539839541 chr13 115169878 5322383 0.04621332498068636 0.2748236314581146 chr14 107349540 4960460 0.04620848864373336 0.2823671431751433 chr15 102531392 4540644 0.04428540285496173 0.26540368553059684 chr16 90354753 5526673 0.061166378264572316 0.8750588555377062 chr17 81195210 4046670 0.04983877743526989 0.4629526849433554 chr18 78077248 4715277 0.06039245901699814 0.8362518691429941 chr19 59128983 2744517 0.04641576534472105 0.839871504551642 chr20 63025520 3373365 0.05352379480565968 0.33256503777515267 chr21 48129895 2280896 0.047390421275591815 0.37834304728608037 chr22 51304566 1568462 0.030571586942183666 0.23145177585698315 chrMT 16571 2775427 167.4869953533281 43.94778329000911 chrX 155270560 4876201 0.03140454314069583 0.25852133454502163 chrY 59373566 2417529 0.040717261280887186 0.9366400547814198