BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354850.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 14,533,674 number of mapped reads = 14,408,979 (99.14%) number of supplementary alignments = 346,953 (2.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,211,131 number of mapped paired reads (second in pair) = 7,197,848 number of mapped paired reads (both in pair) = 14,384,378 number of mapped paired reads (singletons) = 24,601 number of mapped bases = 1,841,075,094 bp number of sequenced bases = 1,840,289,387 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,630,147 duplication rate = 73.63% >>>>>>> Insert size mean insert size = 223,677.0391 std insert size = 5,440,019.852 median insert size = 160 >>>>>>> Mapping quality mean mapping quality = 54.0628 >>>>>>> ACTG content number of A's = 535,856,562 bp (29.12%) number of C's = 374,538,101 bp (20.35%) number of T's = 544,699,195 bp (29.6%) number of G's = 385,190,900 bp (20.93%) number of N's = 4,629 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 11,843,080 number of insertions = 273,850 mapped reads with insertion percentage = 1.8% number of deletions = 296,769 mapped reads with deletion percentage = 1.98% homopolymer indels = 44.23% >>>>>>> Coverage mean coverageData = 0.5947X std coverageData = 16.6199X There is a 11.11% of reference with a coverageData >= 1X There is a 9.98% of reference with a coverageData >= 2X There is a 6.82% of reference with a coverageData >= 3X There is a 6.25% of reference with a coverageData >= 4X There is a 4.3% of reference with a coverageData >= 5X There is a 3.93% of reference with a coverageData >= 6X There is a 2.71% of reference with a coverageData >= 7X There is a 2.46% of reference with a coverageData >= 8X There is a 1.7% of reference with a coverageData >= 9X There is a 1.54% of reference with a coverageData >= 10X There is a 1.07% of reference with a coverageData >= 11X There is a 0.97% of reference with a coverageData >= 12X There is a 0.68% of reference with a coverageData >= 13X There is a 0.61% of reference with a coverageData >= 14X There is a 0.43% of reference with a coverageData >= 15X There is a 0.39% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 148666773 0.5964549753318368 18.10530851470043 chr2 243199373 167866764 0.6902434078232594 52.22069765999213 chr3 198022430 123119929 0.6217473899295145 2.429513670076948 chr4 191154276 129388170 0.6768782404846648 6.410016278899772 chr5 180915260 113054054 0.6249005971082815 2.283313389539435 chr6 171115067 107587947 0.6287461933436873 3.076130149856577 chr7 159138663 100765333 0.6331920295195643 10.014208281793191 chr8 146364022 92317058 0.6307360015017899 3.8169993420567527 chr9 141213431 79773953 0.5649176033404358 9.360088640791464 chr10 135534747 98333830 0.725524872230735 17.37601189407068 chr11 135006516 84665320 0.6271202495144753 3.6017493264626874 chr12 133851895 80206893 0.5992211989228842 2.257218863519326 chr13 115169878 60768415 0.5276415678759336 2.0877793723371525 chr14 107349540 55020633 0.5125372032334745 3.4107648784326035 chr15 102531392 52876389 0.5157092668750659 2.03922254131711 chr16 90354753 52284343 0.5786562550837807 3.900808168211296 chr17 81195210 47510914 0.5851442960736231 3.8284086829798127 chr18 78077248 52819095 0.6764979088402296 8.181211112533273 chr19 59128983 32756430 0.5539826382604957 9.437381842307703 chr20 63025520 36717628 0.5825834995094051 2.9002528724769485 chr21 48129895 24965339 0.5187075309430864 3.824289869138888 chr22 51304566 20816097 0.4057357584897999 2.154875238551969 chrMT 16571 7649085 461.5946533099994 93.90134693652064 chrX 155270560 51606091 0.3323623679852768 1.9182344199689998 chrY 59373566 19538611 0.3290792909423699 8.012590236242174