BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617703.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 49,066,826 number of mapped reads = 48,404,906 (98.65%) number of supplementary alignments = 859,304 (1.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,308,469 number of mapped paired reads (second in pair) = 24,096,437 number of mapped paired reads (both in pair) = 48,040,358 number of mapped paired reads (singletons) = 364,548 number of mapped bases = 6,510,557,224 bp number of sequenced bases = 6,506,183,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,913,094 duplication rate = 20.48% >>>>>>> Insert size mean insert size = 98,358.5233 std insert size = 3,010,115.8034 median insert size = 276 >>>>>>> Mapping quality mean mapping quality = 53.3258 >>>>>>> ACTG content number of A's = 1,930,454,332 bp (29.67%) number of C's = 1,209,399,789 bp (18.59%) number of T's = 1,970,821,033 bp (30.29%) number of G's = 1,395,265,606 bp (21.45%) number of N's = 242,692 bp (0%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 75,906,269 number of insertions = 1,149,768 mapped reads with insertion percentage = 2.23% number of deletions = 2,081,666 mapped reads with deletion percentage = 4.13% homopolymer indels = 45.25% >>>>>>> Coverage mean coverageData = 2.1031X std coverageData = 28.7287X There is a 45.19% of reference with a coverageData >= 1X There is a 32.7% of reference with a coverageData >= 2X There is a 24.06% of reference with a coverageData >= 3X There is a 18.37% of reference with a coverageData >= 4X There is a 14.18% of reference with a coverageData >= 5X There is a 11.13% of reference with a coverageData >= 6X There is a 8.83% of reference with a coverageData >= 7X There is a 7.07% of reference with a coverageData >= 8X There is a 5.71% of reference with a coverageData >= 9X There is a 4.65% of reference with a coverageData >= 10X There is a 3.81% of reference with a coverageData >= 11X There is a 3.14% of reference with a coverageData >= 12X There is a 2.6% of reference with a coverageData >= 13X There is a 2.17% of reference with a coverageData >= 14X There is a 1.82% of reference with a coverageData >= 15X There is a 1.54% of reference with a coverageData >= 16X There is a 1.3% of reference with a coverageData >= 17X There is a 1.11% of reference with a coverageData >= 18X There is a 0.94% of reference with a coverageData >= 19X There is a 0.81% of reference with a coverageData >= 20X There is a 0.7% of reference with a coverageData >= 21X There is a 0.6% of reference with a coverageData >= 22X There is a 0.52% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.4% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.31% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 559906230 2.246358415291571 36.200452427185304 chr2 243199373 653497141 2.6870839876713006 34.74641804360119 chr3 198022430 495999732 2.5047654046059327 4.656224974327444 chr4 191154276 341471205 1.7863644598774238 29.795592399961155 chr5 180915260 370453743 2.0476644314028567 4.392332108912785 chr6 171115067 492029011 2.875427743601328 21.981158106715046 chr7 159138663 366776337 2.3047594474260475 25.551771650242948 chr8 146364022 246701554 1.68553412668586 8.097774888973419 chr9 141213431 308368661 2.1837063147343256 66.38972902174758 chr10 135534747 262681380 1.9381109701706234 50.504274057937394 chr11 135006516 322140933 2.386113963566025 23.75165790488287 chr12 133851895 305054403 2.2790443347850995 8.027881792874673 chr13 115169878 151986548 1.3196727359561846 2.9518891178524904 chr14 107349540 268858706 2.5045166099454175 5.380783354982332 chr15 102531392 181363032 1.7688536989725059 4.968800463795329 chr16 90354753 155785609 1.7241551089182878 29.008447502957623 chr17 81195210 139813879 1.7219473784229389 26.05851468731114 chr18 78077248 210216745 2.6924200120373096 57.597180531070734 chr19 59128983 82283782 1.3915981270978397 18.074884435995703 chr20 63025520 133718614 2.1216582425658688 9.05523990116116 chr21 48129895 90264075 1.8754263852019624 13.818511015825122 chr22 51304566 50684544 0.9879148768162272 3.3083299911335216 chrMT 16571 1643140 99.15756441976947 57.986845049905845 chrX 155270560 291954231 1.8802935405140548 8.103455248781888 chrY 59373566 26903989 0.45313075856013096 33.33994371745057