BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004116.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 = 3,980,065 number of mapped reads = 3,484,092 (87.54%) number of supplementary alignments = 29,371 (0.74%) number of secondary alignments = 0 number of mapped bases = 238,907,023 bp number of sequenced bases = 238,810,033 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 231,935 duplication rate = 5.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2422 >>>>>>> ACTG content number of A's = 67,800,972 bp (28.39%) number of C's = 44,515,239 bp (18.64%) number of T's = 76,595,446 bp (32.07%) number of G's = 49,864,905 bp (20.88%) number of N's = 33,471 bp (0.01%) GC percentage = 39.52% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 2,196,623 number of insertions = 17,978 mapped reads with insertion percentage = 0.51% number of deletions = 58,936 mapped reads with deletion percentage = 1.67% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.0772X std coverageData = 0.7853X There is a 5.59% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% 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 0.01% 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 31086475 0.12471974944447581 1.9089934735592344 chr2 243199373 17958409 0.07384233264450069 0.6090225257737785 chr3 198022430 24604376 0.12425044981015534 0.48865881780639303 chr4 191154276 20183960 0.10558989535761157 0.4191566037657472 chr5 180915260 15279485 0.08445658481213801 0.3741056675832915 chr6 171115067 22699391 0.1326557117264256 0.6911248264357867 chr7 159138663 18648050 0.11718114032414612 1.096980917465487 chr8 146364022 8846928 0.06044469043082186 0.5242068199208451 chr9 141213431 3882566 0.027494311075835273 0.43093247361700865 chr10 135534747 9532627 0.0703334547855835 0.9644798195871525 chr11 135006516 7707817 0.057092185091273666 0.61585876453105 chr12 133851895 8664548 0.06473235212695345 0.3344295372642609 chr13 115169878 3486493 0.03027261173273102 0.22693069363386578 chr14 107349540 9099329 0.08476355837202469 0.37872303668420587 chr15 102531392 2650553 0.02585113640123017 0.20494801826760362 chr16 90354753 3290243 0.036414719655091084 0.3213309600759663 chr17 81195210 2984489 0.036756958938833954 0.2722407668632912 chr18 78077248 5579064 0.07145569474989692 1.1905891183908968 chr19 59128983 3471096 0.05870380013131631 1.1252992934345172 chr20 63025520 6573492 0.10429889352757422 0.4175790322677713 chr21 48129895 1535491 0.03190306149639429 0.24562610301329577 chr22 51304566 2373776 0.04626831849625236 0.2725808733191719 chrMT 16571 110028 6.639792408424356 4.284904807142115 chrX 155270560 8265874 0.05323529457226148 0.3773401290163435 chrY 59373566 392463 0.0066100628013483305 0.1337144048483972