BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777280.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 = 35,494,486 number of mapped reads = 35,058,554 (98.77%) number of supplementary alignments = 1,085,196 (3.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,545,000 number of mapped paired reads (second in pair) = 17,513,554 number of mapped paired reads (both in pair) = 34,888,358 number of mapped paired reads (singletons) = 170,196 number of mapped bases = 3,476,050,031 bp number of sequenced bases = 3,473,547,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,323,269 duplication rate = 42.78% >>>>>>> Insert size mean insert size = 242,480.8681 std insert size = 4,836,366.6515 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 53.6601 >>>>>>> ACTG content number of A's = 924,236,934 bp (26.61%) number of C's = 805,483,084 bp (23.19%) number of T's = 923,020,906 bp (26.57%) number of G's = 804,575,119 bp (23.16%) number of N's = 16,231,041 bp (0.47%) GC percentage = 46.35% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 30,339,160 number of insertions = 974,935 mapped reads with insertion percentage = 2.56% number of deletions = 735,296 mapped reads with deletion percentage = 1.93% homopolymer indels = 32.19% >>>>>>> Coverage mean coverageData = 1.1229X std coverageData = 32.8401X There is a 10.28% of reference with a coverageData >= 1X There is a 5.82% of reference with a coverageData >= 2X There is a 3.81% of reference with a coverageData >= 3X There is a 2.94% of reference with a coverageData >= 4X There is a 2.42% of reference with a coverageData >= 5X There is a 2.1% of reference with a coverageData >= 6X There is a 1.88% of reference with a coverageData >= 7X There is a 1.71% of reference with a coverageData >= 8X There is a 1.58% of reference with a coverageData >= 9X There is a 1.47% of reference with a coverageData >= 10X There is a 1.38% of reference with a coverageData >= 11X There is a 1.31% of reference with a coverageData >= 12X There is a 1.24% of reference with a coverageData >= 13X There is a 1.18% of reference with a coverageData >= 14X There is a 1.13% of reference with a coverageData >= 15X There is a 1.08% of reference with a coverageData >= 16X There is a 1.04% of reference with a coverageData >= 17X There is a 1% of reference with a coverageData >= 18X There is a 0.96% of reference with a coverageData >= 19X There is a 0.93% of reference with a coverageData >= 20X There is a 0.9% of reference with a coverageData >= 21X There is a 0.87% of reference with a coverageData >= 22X There is a 0.84% of reference with a coverageData >= 23X There is a 0.81% of reference with a coverageData >= 24X There is a 0.79% of reference with a coverageData >= 25X There is a 0.77% of reference with a coverageData >= 26X There is a 0.74% of reference with a coverageData >= 27X There is a 0.72% of reference with a coverageData >= 28X There is a 0.7% of reference with a coverageData >= 29X There is a 0.69% of reference with a coverageData >= 30X There is a 0.67% of reference with a coverageData >= 31X There is a 0.65% of reference with a coverageData >= 32X There is a 0.64% of reference with a coverageData >= 33X There is a 0.62% of reference with a coverageData >= 34X There is a 0.61% of reference with a coverageData >= 35X There is a 0.59% of reference with a coverageData >= 36X There is a 0.58% of reference with a coverageData >= 37X There is a 0.57% of reference with a coverageData >= 38X There is a 0.55% of reference with a coverageData >= 39X There is a 0.54% of reference with a coverageData >= 40X There is a 0.53% of reference with a coverageData >= 41X There is a 0.52% of reference with a coverageData >= 42X There is a 0.51% of reference with a coverageData >= 43X There is a 0.5% of reference with a coverageData >= 44X There is a 0.49% of reference with a coverageData >= 45X There is a 0.48% of reference with a coverageData >= 46X There is a 0.47% of reference with a coverageData >= 47X There is a 0.46% of reference with a coverageData >= 48X There is a 0.45% of reference with a coverageData >= 49X There is a 0.44% of reference with a coverageData >= 50X There is a 0.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 351236414 1.4091696646164023 20.17329044358367 chr2 243199373 308335598 1.2678305630335651 72.27986902700214 chr3 198022430 197891222 0.9993374083935845 15.654544233856734 chr4 191154276 133087255 0.6962295470701372 21.42991977506174 chr5 180915260 165062136 0.9123726544681747 18.94880254540935 chr6 171115067 153279465 0.8957683720510713 19.862796822657227 chr7 159138663 225281121 1.4156278352043212 29.7183168329326 chr8 146364022 97195381 0.66406607082716 13.880461793862233 chr9 141213431 118860851 0.8417106656094206 18.86039928656034 chr10 135534747 150758236 1.1123216690698512 61.197012523009995 chr11 135006516 233868440 1.7322752036649847 22.59741441722534 chr12 133851895 211087570 1.5770233958958892 23.878024759877135 chr13 115169878 81676236 0.7091805376402326 13.650798869471178 chr14 107349540 75978999 0.7077720034943792 18.71280390698559 chr15 102531392 154678357 1.5085951139725091 17.056844433618 chr16 90354753 132439663 1.4657741690688924 55.19954476861147 chr17 81195210 154588840 1.9039157605479438 20.654194996391965 chr18 78077248 41416576 0.5304564013321781 11.971586943034065 chr19 59128983 220697553 3.732476728037078 40.82805236629246 chr20 63025520 85805382 1.3614386997521004 16.42513688609542 chr21 48129895 20917569 0.4346065787178634 9.925583493961918 chr22 51304566 43152857 0.8411114324600271 15.505808973409431 chrMT 16571 883978 53.3448796089554 18.110662712931227 chrX 155270560 104467270 0.6728079682329993 13.61363635438512 chrY 59373566 13403062 0.2257412330598435 65.36183437539785