BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365368.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 642,069,020 number of mapped reads = 607,829,124 (94.67%) number of supplementary alignments = 5,229,325 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 303,631,137 number of mapped paired reads (second in pair) = 304,197,987 number of mapped paired reads (both in pair) = 605,274,036 number of mapped paired reads (singletons) = 2,555,088 number of mapped bases = 83,771,501,114 bp number of sequenced bases = 83,711,342,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 298,279,112 duplication rate = 43.66% >>>>>>> Insert size mean insert size = 45,647.6051 std insert size = 2,177,293.241 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 54.6418 >>>>>>> ACTG content number of A's = 22,399,931,254 bp (26.76%) number of C's = 19,263,598,765 bp (23.01%) number of T's = 21,913,246,234 bp (26.18%) number of G's = 20,131,688,792 bp (24.05%) number of N's = 2,877,847 bp (0%) GC percentage = 47.06% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 754,971,836 number of insertions = 12,454,997 mapped reads with insertion percentage = 1.99% number of deletions = 42,375,910 mapped reads with deletion percentage = 6.71% homopolymer indels = 52.32% >>>>>>> Coverage mean coverageData = 27.0607X std coverageData = 80.6614X There is a 66.93% of reference with a coverageData >= 1X There is a 63.24% of reference with a coverageData >= 2X There is a 57.63% of reference with a coverageData >= 3X There is a 54.98% of reference with a coverageData >= 4X There is a 51.36% of reference with a coverageData >= 5X There is a 49.09% of reference with a coverageData >= 6X There is a 46.46% of reference with a coverageData >= 7X There is a 44.53% of reference with a coverageData >= 8X There is a 42.49% of reference with a coverageData >= 9X There is a 40.84% of reference with a coverageData >= 10X There is a 39.17% of reference with a coverageData >= 11X There is a 37.74% of reference with a coverageData >= 12X There is a 36.34% of reference with a coverageData >= 13X There is a 35.1% of reference with a coverageData >= 14X There is a 33.89% of reference with a coverageData >= 15X There is a 32.8% of reference with a coverageData >= 16X There is a 31.75% of reference with a coverageData >= 17X There is a 30.78% of reference with a coverageData >= 18X There is a 29.85% of reference with a coverageData >= 19X There is a 28.98% of reference with a coverageData >= 20X There is a 28.15% of reference with a coverageData >= 21X There is a 27.37% of reference with a coverageData >= 22X There is a 26.62% of reference with a coverageData >= 23X There is a 25.91% of reference with a coverageData >= 24X There is a 25.23% of reference with a coverageData >= 25X There is a 24.58% of reference with a coverageData >= 26X There is a 23.97% of reference with a coverageData >= 27X There is a 23.38% of reference with a coverageData >= 28X There is a 22.81% of reference with a coverageData >= 29X There is a 22.27% of reference with a coverageData >= 30X There is a 21.74% of reference with a coverageData >= 31X There is a 21.24% of reference with a coverageData >= 32X There is a 20.76% of reference with a coverageData >= 33X There is a 20.3% of reference with a coverageData >= 34X There is a 19.85% of reference with a coverageData >= 35X There is a 19.42% of reference with a coverageData >= 36X There is a 19% of reference with a coverageData >= 37X There is a 18.6% of reference with a coverageData >= 38X There is a 18.22% of reference with a coverageData >= 39X There is a 17.84% of reference with a coverageData >= 40X There is a 17.48% of reference with a coverageData >= 41X There is a 17.13% of reference with a coverageData >= 42X There is a 16.79% of reference with a coverageData >= 43X There is a 16.46% of reference with a coverageData >= 44X There is a 16.14% of reference with a coverageData >= 45X There is a 15.83% of reference with a coverageData >= 46X There is a 15.53% of reference with a coverageData >= 47X There is a 15.24% of reference with a coverageData >= 48X There is a 14.96% of reference with a coverageData >= 49X There is a 14.69% of reference with a coverageData >= 50X There is a 14.42% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7738722187 31.047955491352617 97.84831170169501 chr2 243199373 7105327409 29.216059734660583 125.36436929684685 chr3 198022430 5366215222 27.099027226360164 61.06575832657846 chr4 191154276 4139136817 21.653383348850642 60.47113142860019 chr5 180915260 4750488963 26.258088803564718 59.679623952312284 chr6 171115067 4461207977 26.07139193067084 60.29038009742611 chr7 159138663 4237497222 26.627704054545188 63.05815215057461 chr8 146364022 4125762725 28.1883667080425 68.28077228776041 chr9 141213431 3743330760 26.508319594614196 91.19762309870154 chr10 135534747 4260481190 31.434604662670008 91.72080374313651 chr11 135006516 4447211778 32.94071952793745 84.95755617580194 chr12 133851895 3850303715 28.765403097206804 65.15063799870113 chr13 115169878 2165567827 18.80324842403671 48.08040317449631 chr14 107349540 2626423553 24.46609042758823 61.831525275679525 chr15 102531392 2750884049 26.829676212725172 64.67401829899363 chr16 90354753 3134866849 34.695096217019156 124.81458212476639 chr17 81195210 2965707459 36.525645527611786 83.63075941692979 chr18 78077248 2116646958 27.109651175205357 96.35892049588995 chr19 59128983 1953657860 33.04061326405699 85.32133381726956 chr20 63025520 2460741850 39.04357869637569 83.89918906178356 chr21 48129895 1100464901 22.864477493665838 93.52976096986669 chr22 51304566 1665277151 32.45865389447013 81.09796171161958 chrMT 16571 9613109 580.1164081829703 470.3168532734754 chrX 155270560 2160216963 13.912598518354027 36.053322412445816 chrY 59373566 435746620 7.3390676921780305 71.5803832400353