BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234070.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 = 6,398,467 number of mapped reads = 6,026,198 (94.18%) number of supplementary alignments = 43,607 (0.68%) number of secondary alignments = 0 number of mapped bases = 388,954,055 bp number of sequenced bases = 388,802,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 800,580 duplication rate = 11.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5741 >>>>>>> ACTG content number of A's = 100,903,786 bp (25.95%) number of C's = 70,911,475 bp (18.24%) number of T's = 125,449,500 bp (32.27%) number of G's = 91,498,469 bp (23.53%) number of N's = 39,026 bp (0.01%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 2,150,310 number of insertions = 25,407 mapped reads with insertion percentage = 0.42% number of deletions = 86,579 mapped reads with deletion percentage = 1.42% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 0.1256X std coverageData = 1.2242X There is a 8.95% of reference with a coverageData >= 1X There is a 2.31% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% 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 23823213 0.09557935263880446 2.151705103235598 chr2 243199373 20206404 0.08308575696862508 2.1612292957754917 chr3 198022430 40363796 0.2038344646109029 0.6018913484771945 chr4 191154276 7542514 0.03945773099001981 0.39919427315086353 chr5 180915260 26640569 0.14725440518395186 0.5270447870580938 chr6 171115067 28660515 0.1674926439996076 1.0005591902782651 chr7 159138663 24622747 0.1547251091332846 1.7887685625561385 chr8 146364022 27227707 0.18602732165969038 1.4868819191142963 chr9 141213431 14678622 0.10394635904002644 0.943682449507341 chr10 135534747 14393977 0.10620137875049857 0.906627257723369 chr11 135006516 9094726 0.06736508925243283 0.8240489123739889 chr12 133851895 16048319 0.11989609112370056 0.4995721337560575 chr13 115169878 17913019 0.15553562538288007 0.5786289312656976 chr14 107349540 22396493 0.20863147620381048 0.6840658128946551 chr15 102531392 12222283 0.1192052771506311 0.507676429140408 chr16 90354753 8376359 0.09270523931375253 0.5985509328150423 chr17 81195210 11402658 0.14043510694781133 0.6151249176903196 chr18 78077248 8907509 0.11408584739052278 2.3429457303514565 chr19 59128983 10368094 0.17534707133386684 1.2528297656311491 chr20 63025520 10448705 0.16578530411173126 0.6342167362804911 chr21 48129895 10181955 0.21155157309194214 0.6816732119773634 chr22 51304566 4774060 0.09305331615123691 0.3928976679886631 chrMT 16571 138015 8.328706776899402 5.848833673098449 chrX 155270560 17484049 0.11260376081595894 0.6201062887371508 chrY 59373566 1037747 0.01747826633825565 0.34140926206492883