BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124815.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 = 28,104,362 number of mapped reads = 27,797,247 (98.91%) number of supplementary alignments = 138,390 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,932,125 number of mapped paired reads (second in pair) = 13,865,122 number of mapped paired reads (both in pair) = 27,652,186 number of mapped paired reads (singletons) = 145,061 number of mapped bases = 2,398,337,120 bp number of sequenced bases = 2,397,089,070 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,236,990 duplication rate = 13.08% >>>>>>> Insert size mean insert size = 35,350.8078 std insert size = 1,716,865.3362 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.6188 >>>>>>> ACTG content number of A's = 685,681,361 bp (28.6%) number of C's = 430,453,051 bp (17.96%) number of T's = 733,382,329 bp (30.59%) number of G's = 547,552,100 bp (22.84%) number of N's = 20,229 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 18,055,662 number of insertions = 301,428 mapped reads with insertion percentage = 1.06% number of deletions = 732,207 mapped reads with deletion percentage = 2.58% homopolymer indels = 47.21% >>>>>>> Coverage mean coverageData = 0.7747X std coverageData = 12.1218X There is a 28.79% of reference with a coverageData >= 1X There is a 15.77% of reference with a coverageData >= 2X There is a 9.23% of reference with a coverageData >= 3X There is a 5.78% of reference with a coverageData >= 4X There is a 3.76% of reference with a coverageData >= 5X There is a 2.53% of reference with a coverageData >= 6X There is a 1.75% of reference with a coverageData >= 7X There is a 1.23% of reference with a coverageData >= 8X There is a 0.89% of reference with a coverageData >= 9X There is a 0.65% of reference with a coverageData >= 10X There is a 0.49% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 216517652 0.868674473633508 12.8615801994211 chr2 243199373 206411684 0.8487344414329555 10.739547673355633 chr3 198022430 158047126 0.7981273939522912 2.2923287185162944 chr4 191154276 157235572 0.8225584867376966 5.959796550991143 chr5 180915260 143421564 0.7927554812125854 1.8868159438960803 chr6 171115067 135297434 0.7906810099896112 7.284711495971734 chr7 159138663 122921613 0.7724182840470389 10.436847505973446 chr8 146364022 145380503 0.993280322673833 4.076570039555494 chr9 141213431 82052656 0.5810541916512176 10.149781993892761 chr10 135534747 137363566 1.0134933590129473 44.53588854894892 chr11 135006516 85997571 0.6369882991425392 4.859139250713817 chr12 133851895 111983354 0.8366213567615162 1.974564441760227 chr13 115169878 70104239 0.6087029023335424 1.5286083148908933 chr14 107349540 65546659 0.6105909629421794 2.2522507828030234 chr15 102531392 57966514 0.5653538186626784 1.5470737640755163 chr16 90354753 83038913 0.9190320402956556 18.05276172444318 chr17 81195210 48791957 0.6009216184058148 9.726851516236152 chr18 78077248 55725863 0.7137272947939969 9.71534643496117 chr19 59128983 26560325 0.4491929955906734 7.122454460053725 chr20 63025520 64406947 1.0219185339525958 2.604388299909546 chr21 48129895 27878036 0.5792249494830604 3.229641162351522 chr22 51304566 10237252 0.199538809079878 1.0038420827776207 chrMT 16571 462437 27.906402751795305 18.606216527438573 chrX 155270560 176024966 1.1336660729503392 5.753959575078548 chrY 59373566 8962717 0.1509546689514994 10.3644132892393