BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708569.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,604,307 number of mapped reads = 3,773,094 (81.95%) number of supplementary alignments = 94 (0%) number of secondary alignments = 0 number of mapped bases = 188,141,672 bp number of sequenced bases = 188,124,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,142 duplication rate = 0.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4719 >>>>>>> ACTG content number of A's = 58,362,838 bp (31.02%) number of C's = 35,636,724 bp (18.94%) number of T's = 58,153,752 bp (30.91%) number of G's = 35,964,343 bp (19.12%) number of N's = 7,013 bp (0%) GC percentage = 38.06% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 294,581 number of insertions = 12,962 mapped reads with insertion percentage = 0.34% number of deletions = 10,068 mapped reads with deletion percentage = 0.27% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.0608X std coverageData = 0.27X There is a 5.51% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.06% 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 12095834 0.04852880186003629 0.23513551281941408 chr2 243199373 18223173 0.07493100321438739 0.2951301683864906 chr3 198022430 13986927 0.07063304394355731 0.2838191838888472 chr4 191154276 14219430 0.07438719288706887 0.29066302220948087 chr5 180915260 16268999 0.08992607367670367 0.32336907556539163 chr6 171115067 11652864 0.06809957886408682 0.2767286038425252 chr7 159138663 11123683 0.06989931164622139 0.2839126458355575 chr8 146364022 8880626 0.06067492460681355 0.26147994741675945 chr9 141213431 7913365 0.0560383310848102 0.2522473101055567 chr10 135534747 6997419 0.051628229327790015 0.24173256319939423 chr11 135006516 9220800 0.06829892566074366 0.38127353730692265 chr12 133851895 7983402 0.05964354856537519 0.26118665574238853 chr13 115169878 7631990 0.0662672404671645 0.27619128643194185 chr14 107349540 7958261 0.07413409503198616 0.3006590982845587 chr15 102531392 5017262 0.04893391089433371 0.2371689610621074 chr16 90354753 2930315 0.03243122141012327 0.18933540427160245 chr17 81195210 2944234 0.03626117846114321 0.20095345647270652 chr18 78077248 6144520 0.07869795820672368 0.2996940544337151 chr19 59128983 1271608 0.021505663305590762 0.15217533337861586 chr20 63025520 3085481 0.048956057800078445 0.2353994559075354 chr21 48129895 1744500 0.03624566394753199 0.20182876412175715 chr22 51304566 1147561 0.022367619287530862 0.15741343823624215 chrMT 16571 50 0.003017319413433106 0.05484719862481972 chrX 155270560 9449278 0.06085685528538056 0.26703024904955247 chrY 59373566 250090 0.004212143835187531 0.0683314061660274