BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777301.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,767,708 number of mapped reads = 1,716,191 (97.09%) number of supplementary alignments = 67,542 (3.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 860,510 number of mapped paired reads (second in pair) = 855,681 number of mapped paired reads (both in pair) = 1,706,432 number of mapped paired reads (singletons) = 9,759 number of mapped bases = 164,080,485 bp number of sequenced bases = 164,011,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,282 duplication rate = 8.96% >>>>>>> Insert size mean insert size = 177,887.6164 std insert size = 4,061,691.3013 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 52.8557 >>>>>>> ACTG content number of A's = 48,398,038 bp (29.51%) number of C's = 33,690,524 bp (20.54%) number of T's = 47,388,599 bp (28.89%) number of G's = 34,531,331 bp (21.05%) number of N's = 2,698 bp (0%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,120,544 number of insertions = 38,178 mapped reads with insertion percentage = 2.15% number of deletions = 24,513 mapped reads with deletion percentage = 1.37% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.8744X There is a 3.59% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 13392850 0.053732463920320585 1.5116169370775867 chr2 243199373 14770434 0.06073384901366501 0.6664965353979576 chr3 198022430 11027513 0.055688201584032676 0.35528140404227276 chr4 191154276 11352918 0.0593913891834677 0.7597209618810324 chr5 180915260 10109750 0.0558811346262333 0.3064059986039096 chr6 171115067 9584771 0.05601360048557267 0.377412873527809 chr7 159138663 6361111 0.03997212795485155 0.6291081582062462 chr8 146364022 8416234 0.05750206837032669 0.4278100179397883 chr9 141213431 6866773 0.04862691141609611 0.6916979748246493 chr10 135534747 9341310 0.06892188318321057 2.0719742308262554 chr11 135006516 7536475 0.05582304634837033 0.3744583445431361 chr12 133851895 7338541 0.0548258282036276 0.30108677387375193 chr13 115169878 5243924 0.04553207914312456 0.27189102650135394 chr14 107349540 4810021 0.044807094655459165 0.27902009992583493 chr15 102531392 4399486 0.042908673277351 0.2611931568637029 chr16 90354753 5392694 0.05968356750419095 0.862071589305105 chr17 81195210 3927966 0.04837681927295957 0.4176937973502871 chr18 78077248 4591167 0.05880287942525843 0.8232893566903104 chr19 59128983 2686406 0.045432981656390065 0.8385186283705335 chr20 63025520 3403114 0.05399580995127053 0.33740377135802263 chr21 48129895 2216433 0.04605106659800525 0.3853560731324257 chr22 51304566 1552145 0.0302535450743312 0.2287978343312902 chrMT 16571 2696599 162.730010258886 40.56666075652367 chrX 155270560 4702222 0.030284053847683682 0.24835964612586184 chrY 59373566 2359628 0.039742062991466605 0.9195137901541139