BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081924.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,813,471 number of mapped reads = 2,566,207 (91.21%) number of supplementary alignments = 18,237 (0.65%) number of secondary alignments = 0 number of mapped bases = 172,187,601 bp number of sequenced bases = 172,116,035 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,011 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3486 >>>>>>> ACTG content number of A's = 47,518,587 bp (27.61%) number of C's = 32,159,749 bp (18.68%) number of T's = 53,709,638 bp (31.21%) number of G's = 38,706,720 bp (22.49%) number of N's = 21,341 bp (0.01%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,392,356 number of insertions = 12,691 mapped reads with insertion percentage = 0.49% number of deletions = 40,798 mapped reads with deletion percentage = 1.57% homopolymer indels = 46.7% >>>>>>> Coverage mean coverageData = 0.0556X std coverageData = 0.5846X There is a 4.75% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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% 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 16079909 0.06451301479405341 1.1263558219791534 chr2 243199373 14716564 0.06051234350838561 0.850807862675751 chr3 198022430 10330781 0.05216975167914059 0.2601344246283306 chr4 191154276 8931691 0.04672503899415779 0.26725806821173836 chr5 180915260 8799502 0.04863880470890073 0.2541890829416653 chr6 171115067 14416133 0.08424818020262353 0.4504368904563575 chr7 159138663 11773651 0.0739835988191003 0.8643129746842201 chr8 146364022 10158011 0.06940237676715388 0.6750906485763652 chr9 141213431 8344681 0.05909268644566819 0.6080437806713409 chr10 135534747 6979965 0.05149945054311423 0.5682626451462831 chr11 135006516 7751905 0.057418747106991484 0.4170085557573967 chr12 133851895 7598286 0.056766368529933775 0.28712796811952274 chr13 115169878 4220187 0.03664314900116505 0.21563453126342377 chr14 107349540 4347193 0.04049568353995742 0.28234822483976424 chr15 102531392 2897509 0.028259725567755873 0.1979687355516865 chr16 90354753 3974291 0.04398541159201664 0.2999688440656414 chr17 81195210 5005233 0.061644436907054 0.32492243419497185 chr18 78077248 5060474 0.06481368298226904 0.931371390673638 chr19 59128983 4101124 0.0693589470327944 0.8426637495502838 chr20 63025520 4533091 0.07192469018899011 0.3161072955376889 chr21 48129895 1872091 0.03889663586425859 0.26785286017475524 chr22 51304566 1417919 0.027637286708555336 0.18444549498675905 chrMT 16571 53770 3.244825297205962 2.594890237634634 chrX 155270560 8426717 0.05427118315281403 0.33902452455408744 chrY 59373566 396923 0.006685180405030751 0.16475011384626545