BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006048.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 5,352,700 number of mapped reads = 4,602,002 (85.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,347,187 number of mapped paired reads (second in pair) = 2,254,815 number of mapped paired reads (both in pair) = 4,173,682 number of mapped paired reads (singletons) = 428,320 number of mapped bases = 177,529,332 bp number of sequenced bases = 177,510,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 224,830 duplication rate = 4.47% >>>>>>> Insert size mean insert size = 68,526.4406 std insert size = 2,579,360.869 median insert size = 87 >>>>>>> Mapping quality mean mapping quality = 46.1174 >>>>>>> ACTG content number of A's = 47,381,686 bp (26.69%) number of C's = 39,775,836 bp (22.41%) number of T's = 48,840,051 bp (27.51%) number of G's = 41,442,484 bp (23.35%) number of N's = 70,942 bp (0.04%) GC percentage = 45.75% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,080,404 number of insertions = 5,644 mapped reads with insertion percentage = 0.12% number of deletions = 14,549 mapped reads with deletion percentage = 0.32% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 0.0573X std coverageData = 0.3738X There is a 3.7% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% 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 15256998 0.06121147437381911 0.4004606184949471 chr2 243199373 15302175 0.0629202896834771 0.4095798247716435 chr3 198022430 12128057 0.0612458750253696 0.3531317963796889 chr4 191154276 10808869 0.05654526399398986 0.35038100397043104 chr5 180915260 10612255 0.058658705738808326 0.345375095253175 chr6 171115067 10222197 0.05973873124802037 0.3936855218723296 chr7 159138663 9753514 0.06128940520255596 0.427940093844452 chr8 146364022 8737153 0.05969467687899421 0.38986364432725934 chr9 141213431 7591029 0.05375571534693467 0.3476129907641408 chr10 135534747 8679180 0.06403656768548069 0.3756471582772826 chr11 135006516 8295475 0.06144499721776392 0.4942234232891511 chr12 133851895 8205091 0.061299774650183325 0.3552926570464116 chr13 115169878 5408723 0.046963000169193546 0.3108289281042339 chr14 107349540 5441177 0.050686542299109995 0.3253263442543986 chr15 102531392 5485732 0.053502950589025454 0.3346012783298122 chr16 90354753 5766729 0.06382319477980311 0.38076577384007193 chr17 81195210 5530874 0.06811823012712204 0.3995536575076119 chr18 78077248 4563066 0.058442966637348694 0.3935769198221075 chr19 59128983 4155099 0.07027178194490509 0.4369791963068747 chr20 63025520 4274523 0.06782209809613629 0.37971428551748343 chr21 48129895 2373110 0.049306361462039344 0.3422404163112197 chr22 51304566 2464383 0.04803437963007035 0.33665911711752394 chrMT 16571 12387 0.7475107114839177 1.2250667000948994 chrX 155270560 5314733 0.0342288518828038 0.2700106331453856 chrY 59373566 1146803 0.019315043330899142 0.20716952614039355