BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006381.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 = 6,901,950 number of mapped reads = 6,159,492 (89.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,122,807 number of mapped paired reads (second in pair) = 3,036,685 number of mapped paired reads (both in pair) = 5,678,024 number of mapped paired reads (singletons) = 481,468 number of mapped bases = 238,575,585 bp number of sequenced bases = 238,546,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,732 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 75,659.6927 std insert size = 2,633,839.7153 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 48.3038 >>>>>>> ACTG content number of A's = 66,561,741 bp (27.9%) number of C's = 51,430,079 bp (21.56%) number of T's = 67,477,771 bp (28.29%) number of G's = 53,066,507 bp (22.25%) number of N's = 10,157 bp (0%) GC percentage = 43.81% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 877,284 number of insertions = 6,379 mapped reads with insertion percentage = 0.1% number of deletions = 21,970 mapped reads with deletion percentage = 0.36% homopolymer indels = 44.69% >>>>>>> Coverage mean coverageData = 0.0771X std coverageData = 0.4086X There is a 6.46% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% 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% 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 19293514 0.07740608196919999 0.49675733687953755 chr2 243199373 20690900 0.08507793315733589 0.4058742590415124 chr3 198022430 16157694 0.08159527180835019 0.3259591210433634 chr4 191154276 14926989 0.07808870045889008 0.3551000788015818 chr5 180915260 14242769 0.07872618926673183 0.3194124449399291 chr6 171115067 13519240 0.07900671891154974 0.3487528558666891 chr7 159138663 12777903 0.08029414574131492 0.45417450887005 chr8 146364022 11995306 0.08195529089792299 0.8115655257156894 chr9 141213431 10098044 0.07150909037823747 0.3456446969979768 chr10 135534747 11395296 0.08407656525156608 0.44329436340422257 chr11 135006516 10666059 0.07900403118320601 0.3733262193535544 chr12 133851895 11075027 0.08274090553592835 0.3319539076960879 chr13 115169878 6939704 0.06025624165374214 0.28162527640515594 chr14 107349540 7342327 0.06839644585342425 0.3130981832508409 chr15 102531392 6479519 0.06319546505327851 0.287448571273478 chr16 90354753 7273038 0.08049424915145305 0.38038033278092837 chr17 81195210 6841825 0.08426389931130174 0.3462601921935517 chr18 78077248 6349255 0.08132016896907023 0.5210109940293992 chr19 59128983 5177318 0.08755973360813596 0.43928879545849947 chr20 63025520 5567381 0.08833534415900099 0.3546668409511939 chr21 48129895 3006613 0.06246872136330237 0.32687828233868355 chr22 51304566 2765215 0.05389802927092298 0.2720098178843874 chrMT 16571 24121 1.455615231428399 1.6856289532202575 chrX 155270560 13356590 0.08602139388175067 0.35671468377232934 chrY 59373566 613938 0.010340258154613789 0.2528221673131482