BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013170.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,812,769 number of mapped reads = 1,219,147 (67.25%) number of supplementary alignments = 10,671 (0.59%) number of secondary alignments = 0 number of mapped bases = 76,040,028 bp number of sequenced bases = 75,964,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 220,599 duplication rate = 13.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7905 >>>>>>> ACTG content number of A's = 20,641,272 bp (27.17%) number of C's = 13,554,466 bp (17.84%) number of T's = 24,492,257 bp (32.24%) number of G's = 17,163,571 bp (22.59%) number of N's = 112,647 bp (0.15%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 860,379 number of insertions = 5,283 mapped reads with insertion percentage = 0.43% number of deletions = 43,166 mapped reads with deletion percentage = 3.46% homopolymer indels = 43% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.33X There is a 1.27% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 5100322 0.020462625045977317 0.47664271194701774 chr2 243199373 7510182 0.03088076218025447 0.3754220584509257 chr3 198022430 5013211 0.025316379563668622 0.2800704125585636 chr4 191154276 7039904 0.03682838881406974 0.3543610132248075 chr5 180915260 4027453 0.022261543885242183 0.2589973209910088 chr6 171115067 3502993 0.020471563734361275 0.27573842428307543 chr7 159138663 5255629 0.0330254691155725 0.4025228637011113 chr8 146364022 5150021 0.03518638617350923 0.46719105110209264 chr9 141213431 1757388 0.012444906887079318 0.2141745450283632 chr10 135534747 4229341 0.03120484668038669 0.35854115949191384 chr11 135006516 3371290 0.024971313236466307 0.2858429472076337 chr12 133851895 2593286 0.019374294252614055 0.23758534564378928 chr13 115169878 1868885 0.016227203088640937 0.22248703533579792 chr14 107349540 2631741 0.02451562437994611 0.2879351950624078 chr15 102531392 1591917 0.015526142471566171 0.2147378042068657 chr16 90354753 2295299 0.025403190466360966 0.2886240320179095 chr17 81195210 1452363 0.017887299016776975 0.23084501047322334 chr18 78077248 2127065 0.027243083670162146 0.42266036937001267 chr19 59128983 893820 0.015116444671473548 0.36562305626278485 chr20 63025520 1243539 0.019730721777464114 0.25100421867156475 chr21 48129895 1284444 0.026687031002249225 0.29561127719907027 chr22 51304566 554138 0.010800948983761017 0.1736860079527639 chrMT 16571 50544 3.050147848651258 3.449266247737317 chrX 155270560 5268041 0.03392813808361353 0.3339429078973214 chrY 59373566 227212 0.0038268208448183827 0.10232463510722271