BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046489.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 10,103,356 number of mapped reads = 10,056,497 (99.54%) number of supplementary alignments = 50,034 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,035,830 number of mapped paired reads (second in pair) = 5,020,667 number of mapped paired reads (both in pair) = 10,024,590 number of mapped paired reads (singletons) = 31,907 number of mapped bases = 966,745,370 bp number of sequenced bases = 966,520,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,546,729 duplication rate = 38.31% >>>>>>> Insert size mean insert size = 16,513.9191 std insert size = 1,243,297.2333 median insert size = 129 >>>>>>> Mapping quality mean mapping quality = 52.8979 >>>>>>> ACTG content number of A's = 282,807,751 bp (29.26%) number of C's = 201,724,744 bp (20.87%) number of T's = 281,091,369 bp (29.08%) number of G's = 200,819,641 bp (20.78%) number of N's = 76,544 bp (0.01%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 3,801,018 number of insertions = 71,789 mapped reads with insertion percentage = 0.7% number of deletions = 83,393 mapped reads with deletion percentage = 0.8% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.3123X std coverageData = 26.3578X There is a 3.1% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 166878239 0.6695198524700967 32.891392205289065 chr2 243199373 68733125 0.28262048603225637 18.658939485989357 chr3 198022430 40177658 0.20289448018590622 11.34139514338189 chr4 191154276 56065165 0.293297990362507 31.513742787272463 chr5 180915260 79137216 0.43742698100757227 31.84425557591981 chr6 171115067 82102382 0.47980802298373876 46.2248660333848 chr7 159138663 48981793 0.3077931665166748 19.467847923963287 chr8 146364022 137495955 0.9394108819994028 49.94959788491616 chr9 141213431 13691594 0.09695674060918469 8.698067823155178 chr10 135534747 41121633 0.30340288309978547 38.91439226368676 chr11 135006516 12727416 0.09427260533113824 6.651300463991135 chr12 133851895 23546631 0.1759155595070208 10.953452921654478 chr13 115169878 20127228 0.17476121664381722 16.20728685507835 chr14 107349540 29234477 0.2723297836208707 18.599140672220948 chr15 102531392 15400753 0.15020524640882668 8.47769229598044 chr16 90354753 41697537 0.4614869236596773 34.6601268355375 chr17 81195210 27866921 0.3432089282114056 18.652730198602875 chr18 78077248 5947779 0.07617813322518745 2.9873016225672604 chr19 59128983 3743267 0.06330680505700563 2.360779851691592 chr20 63025520 8425175 0.133678785990183 8.47179055015665 chr21 48129895 6858811 0.1425062531302011 19.44343760977514 chr22 51304566 2760625 0.053808563549684836 4.19352947945712 chrMT 16571 53299 3.2164021483314222 2.3614260593200624 chrX 155270560 33774517 0.21752041726390373 29.175549999749656 chrY 59373566 196174 0.0033040629562320714 0.29249122148278434