BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926935.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 12,690,538 number of mapped reads = 12,323,312 (97.11%) number of supplementary alignments = 288,226 (2.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,175,938 number of mapped paired reads (second in pair) = 6,147,374 number of mapped paired reads (both in pair) = 12,136,332 number of mapped paired reads (singletons) = 186,980 number of mapped bases = 1,119,195,618 bp number of sequenced bases = 1,118,327,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 744,889 duplication rate = 4.95% >>>>>>> Insert size mean insert size = 228,176.1178 std insert size = 4,597,457.8487 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 52.6333 >>>>>>> ACTG content number of A's = 315,746,812 bp (28.23%) number of C's = 219,748,072 bp (19.65%) number of T's = 322,778,123 bp (28.86%) number of G's = 259,998,079 bp (23.25%) number of N's = 55,982 bp (0.01%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 10,607,795 number of insertions = 193,459 mapped reads with insertion percentage = 1.54% number of deletions = 591,095 mapped reads with deletion percentage = 4.67% homopolymer indels = 51.98% >>>>>>> Coverage mean coverageData = 0.3615X std coverageData = 1.4247X There is a 20.62% of reference with a coverageData >= 1X There is a 8.26% of reference with a coverageData >= 2X There is a 3.39% of reference with a coverageData >= 3X There is a 1.59% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 79735790 0.31990207157798817 1.9071003109000113 chr2 243199373 86038427 0.35377733889141233 2.1995852316427635 chr3 198022430 67082252 0.3387608767350244 0.8458503271311404 chr4 191154276 58464668 0.30585069412729227 1.3573191754645362 chr5 180915260 59286809 0.32770485474801847 0.827486685189764 chr6 171115067 57353773 0.3351766387702142 1.3421482176487907 chr7 159138663 51702401 0.32488899947588473 1.032507815389945 chr8 146364022 49719520 0.33969768882136897 0.9166764993181993 chr9 141213431 42464675 0.30071272044937425 1.529440204617076 chr10 135534747 93818359 0.6922089063994785 2.353801670754382 chr11 135006516 91392419 0.676948207448002 1.7824962579510828 chr12 133851895 43875415 0.32779076456108447 0.8610874671431208 chr13 115169878 56719930 0.4924892774480494 1.1490933269838677 chr14 107349540 29606000 0.27579065546065684 0.7806317626342321 chr15 102531392 28823180 0.28111566065542154 0.7780711484174246 chr16 90354753 30564638 0.338273715384956 1.3782626974951933 chr17 81195210 26222761 0.3229594578300863 0.9762999460746026 chr18 78077248 25670727 0.32878626818404255 1.5348117407752888 chr19 59128983 32896725 0.5563553325447861 1.558627939365809 chr20 63025520 22751994 0.3609965296597315 0.9413844078829101 chr21 48129895 12846598 0.2669151470203706 1.2151031559066243 chr22 51304566 12590670 0.24541032078899178 0.7605193224340278 chrMT 16571 949718 57.31205117373725 46.06623882238912 chrX 155270560 56625256 0.36468765231477235 0.9718730654811996 chrY 59373566 1992913 0.03356566119003194 1.1593611501493597