BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004027.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 = 2,574,907 number of mapped reads = 2,276,901 (88.43%) number of supplementary alignments = 15,801 (0.61%) number of secondary alignments = 0 number of mapped bases = 148,566,805 bp number of sequenced bases = 148,502,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,647 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2517 >>>>>>> ACTG content number of A's = 40,197,862 bp (27.07%) number of C's = 27,473,695 bp (18.5%) number of T's = 46,092,880 bp (31.04%) number of G's = 34,715,481 bp (23.38%) number of N's = 22,136 bp (0.01%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,354,635 number of insertions = 11,869 mapped reads with insertion percentage = 0.52% number of deletions = 39,627 mapped reads with deletion percentage = 1.72% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.048X std coverageData = 0.4708X There is a 4.15% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% 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% 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 14079275 0.05648641894456905 0.9840124286626162 chr2 243199373 13080860 0.05378656958955236 0.5377524992760875 chr3 198022430 10940262 0.05524758988161089 0.26366977710905304 chr4 191154276 9593779 0.050188670642136196 0.2650535734252005 chr5 180915260 10077848 0.055704797925835554 0.2684802699069343 chr6 171115067 8740552 0.051079967142811565 0.298793588523929 chr7 159138663 9462529 0.0594609054871851 0.7301676531276173 chr8 146364022 11379887 0.07775057588947644 0.5004131966919072 chr9 141213431 5147152 0.036449450760813254 0.4202467099918518 chr10 135534747 6905538 0.05095031460825319 0.43108036084263374 chr11 135006516 5551397 0.041119474559287196 0.3310689985899351 chr12 133851895 5734374 0.04284118652186433 0.24465308022935334 chr13 115169878 4605569 0.039989353813503214 0.23252987210519405 chr14 107349540 2690219 0.025060368213967194 0.24236271534553072 chr15 102531392 4936486 0.048146093637351575 0.257506321595339 chr16 90354753 3205147 0.03547292083239938 0.2704933255101237 chr17 81195210 3279750 0.04039339266441949 0.24912187696304938 chr18 78077248 3828170 0.049030544724117324 0.7490119173683222 chr19 59128983 2645531 0.04474169630145677 0.6770736647074199 chr20 63025520 2592788 0.04113870064062938 0.24934106685294438 chr21 48129895 1429998 0.029711222100110544 0.22122062507668347 chr22 51304566 1295455 0.025250286689882533 0.17482287704984956 chrMT 16571 42469 2.5628507633818116 2.5643114965826057 chrX 155270560 6972550 0.04490580828716017 0.29120102211948984 chrY 59373566 349220 0.00588174205335755 0.12155058061510098