BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777268.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 3,283,582 number of mapped reads = 3,067,914 (93.43%) number of supplementary alignments = 54,730 (1.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,539,459 number of mapped paired reads (second in pair) = 1,528,455 number of mapped paired reads (both in pair) = 3,043,454 number of mapped paired reads (singletons) = 24,460 number of mapped bases = 228,941,348 bp number of sequenced bases = 228,898,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,205 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 195,064.8951 std insert size = 4,265,921.7101 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 52.5162 >>>>>>> ACTG content number of A's = 68,161,798 bp (29.78%) number of C's = 46,543,453 bp (20.33%) number of T's = 66,716,996 bp (29.15%) number of G's = 47,463,154 bp (20.74%) number of N's = 13,393 bp (0.01%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,289,535 number of insertions = 50,153 mapped reads with insertion percentage = 1.62% number of deletions = 21,300 mapped reads with deletion percentage = 0.69% homopolymer indels = 49.53% >>>>>>> Coverage mean coverageData = 0.074X std coverageData = 0.3809X There is a 6.13% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.12% 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% 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 19043804 0.07640423892865647 0.5062750618690539 chr2 243199373 21669921 0.08910352330554734 0.36177762902960003 chr3 198022430 15554924 0.07855132370610743 0.3198128753614808 chr4 191154276 14381312 0.07523405858836242 0.3165372891528535 chr5 180915260 15754552 0.08708249375978566 0.3346605482677976 chr6 171115067 11042818 0.0645344573894244 0.3179714552467478 chr7 159138663 15736420 0.09888495795644582 0.40595812985030894 chr8 146364022 11637957 0.07951378242393475 0.3276182779731347 chr9 141213431 8400447 0.059487592224850054 0.4636216416517919 chr10 135534747 10303835 0.0760235675948102 0.41595150562405486 chr11 135006516 13356736 0.09893400997030395 0.37288192232998113 chr12 133851895 10646337 0.07953818659048495 0.31983224178276487 chr13 115169878 10024323 0.08703945140933465 0.3358314768198184 chr14 107349540 4575975 0.04262687106064916 0.23474012089122467 chr15 102531392 8284687 0.08080146810061839 0.3242438865621688 chr16 90354753 5790795 0.06408954490750475 0.3201010922500372 chr17 81195210 5337566 0.06573744929041997 0.3160654440739846 chr18 78077248 4949433 0.0633914889008383 0.40184400180589464 chr19 59128983 3993209 0.06753386913487079 0.37824397713459373 chr20 63025520 5937089 0.09420134891390028 0.3497277270117623 chr21 48129895 2047152 0.042533897071664085 0.24297144090452796 chr22 51304566 1591869 0.031027823137613132 0.20015940345376193 chrMT 16571 932442 56.269506970007846 13.596259580446297 chrX 155270560 7651947 0.04928137697191277 0.25631948230106605 chrY 59373566 295798 0.00498198137534808 0.1286866540334999