BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548950.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,766,216 number of mapped reads = 8,341,845 (85.42%) number of secondary alignments = 0 number of mapped bases = 330,902,775 bp number of sequenced bases = 330,871,868 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 451,053 duplication rate = 4.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2087 >>>>>>> ACTG content number of A's = 94,381,834 bp (28.53%) number of C's = 70,193,344 bp (21.21%) number of T's = 95,500,369 bp (28.86%) number of G's = 70,795,801 bp (21.4%) number of N's = 520 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0022 number of mismatches = 733,407 number of insertions = 8,933 mapped reads with insertion percentage = 0.11% number of deletions = 22,990 mapped reads with deletion percentage = 0.28% homopolymer indels = 43% >>>>>>> Coverage mean coverageData = 0.1069X std coverageData = 1.1541X There is a 7.61% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% 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% 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 27069799 0.10860474044716623 1.410422887541112 chr2 243199373 28293524 0.11633880322545075 0.6110154155528013 chr3 198022430 22787555 0.11507562552383586 0.4496131932159292 chr4 191154276 21298139 0.11141858526879095 0.46577149694621056 chr5 180915260 20635397 0.11406111900123848 0.45157516466366143 chr6 171115067 19308383 0.11283859065432268 0.4677782046246594 chr7 159138663 18852958 0.11846874696942754 1.1716808341376552 chr8 146364022 17529983 0.11976975461906889 4.258375400280055 chr9 141213431 14083826 0.09973432342990095 0.5624389706864481 chr10 135534747 15843231 0.1168942381985632 0.5859032735968165 chr11 135006516 15349742 0.11369630485094512 0.6438078725805894 chr12 133851895 15305974 0.11435007326567921 0.45603374937575175 chr13 115169878 10661558 0.09257245197394409 0.39790988226343826 chr14 107349540 10241254 0.09540100497868924 0.4582227416924061 chr15 102531392 9768322 0.09527152425668814 0.4049932397279591 chr16 90354753 9635822 0.10664432893751588 0.46316954204897864 chr17 81195210 9089748 0.11194931326613972 0.4660032634856635 chr18 78077248 8914404 0.11417415736784166 0.9908971702989595 chr19 59128983 6638599 0.11227318081895642 1.1064128256279564 chr20 63025520 7366362 0.11687903566682195 0.4662600554046787 chr21 48129895 4381927 0.09104376811958555 0.48877551768983335 chr22 51304566 4076233 0.07945166128098619 0.5471984806117942 chrMT 16571 23534 1.4201919015146944 2.167521633477905 chrX 155270560 10626031 0.06843558109148315 0.4238158206660484 chrY 59373566 3120470 0.052556553534278204 0.5875190413186636