BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927056.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 = 32,346,944 number of mapped reads = 31,664,430 (97.89%) number of supplementary alignments = 813,326 (2.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,884,678 number of mapped paired reads (second in pair) = 15,779,752 number of mapped paired reads (both in pair) = 31,252,976 number of mapped paired reads (singletons) = 411,454 number of mapped bases = 2,916,660,643 bp number of sequenced bases = 2,914,595,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,297,465 duplication rate = 6.24% >>>>>>> Insert size mean insert size = 219,674.885 std insert size = 4,690,221.5693 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 52.924 >>>>>>> ACTG content number of A's = 819,097,561 bp (28.1%) number of C's = 586,159,846 bp (20.11%) number of T's = 834,647,932 bp (28.64%) number of G's = 674,280,145 bp (23.13%) number of N's = 409,795 bp (0.01%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 29,705,781 number of insertions = 451,298 mapped reads with insertion percentage = 1.4% number of deletions = 1,451,361 mapped reads with deletion percentage = 4.47% homopolymer indels = 52.31% >>>>>>> Coverage mean coverageData = 0.9422X std coverageData = 60.7672X There is a 33.28% of reference with a coverageData >= 1X There is a 18.28% of reference with a coverageData >= 2X There is a 10.53% of reference with a coverageData >= 3X There is a 6.46% of reference with a coverageData >= 4X There is a 4.1% of reference with a coverageData >= 5X There is a 2.68% of reference with a coverageData >= 6X There is a 1.79% of reference with a coverageData >= 7X There is a 1.22% of reference with a coverageData >= 8X There is a 0.85% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 228145913 0.915327360408061 13.456066519922066 chr2 243199373 213792118 0.8790816989482946 4.41044203447752 chr3 198022430 168720634 0.8520278940118047 1.737794975554444 chr4 191154276 148189233 0.7752336808829743 2.289694679117948 chr5 180915260 149789018 0.8279512629282902 1.9208687951083567 chr6 171115067 143195908 0.8368398558380601 1.7424615542939643 chr7 159138663 130919089 0.8226730483465228 2.1233741727992523 chr8 146364022 124945685 0.8536639215885992 1.999692041836841 chr9 141213431 107265983 0.759601846937633 2.9728852909797947 chr10 135534747 123003750 0.9075440263300156 5.348598683443378 chr11 135006516 124481410 0.9220400147204747 2.4133752142183007 chr12 133851895 115733361 0.864637448726445 1.7973690117412728 chr13 115169878 73723335 0.6401268828295538 5.047242057326523 chr14 107349540 77496486 0.7219079466945084 1.6649566545940426 chr15 102531392 73644810 0.7182659726301189 1.6356927782170425 chr16 90354753 84304412 0.9330379332673291 4.107198290752379 chr17 81195210 80494474 0.991369737204941 9.056359635769564 chr18 78077248 64468691 0.8257039361838163 2.968531264358262 chr19 59128983 55712413 0.9422183533919398 2.5552732501998006 chr20 63025520 62217024 0.9871719265465798 2.0605072910378595 chr21 48129895 32792229 0.6813276654769349 2.632108405809393 chr22 51304566 39123649 0.7625763562642748 1.9615629917233586 chrMT 16571 351871618 21234.181280550358 15323.380530030356 chrX 155270560 137860413 0.8878721954760773 1.9385646253111404 chrY 59373566 4768987 0.08032172094901627 3.1532253787395272