BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926959.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 = 10,499,394 number of mapped reads = 10,036,278 (95.59%) number of supplementary alignments = 443,968 (4.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,021,551 number of mapped paired reads (second in pair) = 5,014,727 number of mapped paired reads (both in pair) = 9,817,962 number of mapped paired reads (singletons) = 218,316 number of mapped bases = 901,348,341 bp number of sequenced bases = 900,671,814 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 702,845 duplication rate = 5.88% >>>>>>> Insert size mean insert size = 453,196.8401 std insert size = 6,584,319.9622 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 52.292 >>>>>>> ACTG content number of A's = 255,209,590 bp (28.34%) number of C's = 176,152,178 bp (19.56%) number of T's = 257,589,695 bp (28.6%) number of G's = 211,673,487 bp (23.5%) number of N's = 46,864 bp (0.01%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 9,098,350 number of insertions = 155,287 mapped reads with insertion percentage = 1.52% number of deletions = 454,081 mapped reads with deletion percentage = 4.41% homopolymer indels = 51.9% >>>>>>> Coverage mean coverageData = 0.2912X std coverageData = 1.1409X There is a 17.48% of reference with a coverageData >= 1X There is a 6.6% of reference with a coverageData >= 2X There is a 2.53% of reference with a coverageData >= 3X There is a 1.11% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 70824088 0.2841480904474858 1.2257272738412892 chr2 243199373 74907707 0.30800945773819904 2.0135420356485487 chr3 198022430 62703537 0.3166486594473161 0.820917082214157 chr4 191154276 55738930 0.29159133222842476 1.2596068422371511 chr5 180915260 55053177 0.3043036668106383 0.7978081167092542 chr6 171115067 52327851 0.30580504637852846 0.8378692877409338 chr7 159138663 47503702 0.29850509677839887 0.8582022655224346 chr8 146364022 45961405 0.3140211943615488 0.8670989471184527 chr9 141213431 36073787 0.2554557788486847 1.0059583104228453 chr10 135534747 45349211 0.3345947220457054 1.7866839674357355 chr11 135006516 44080032 0.32650299634426533 1.1515764456182016 chr12 133851895 41023091 0.3064812119395097 1.210597844877358 chr13 115169878 27197801 0.236153771040723 0.7060400035389099 chr14 107349540 28074501 0.2615241853854241 0.7587082207064765 chr15 102531392 38374119 0.3742670244835845 0.9687611560499886 chr16 90354753 14186071 0.1570041478614855 0.815811796948516 chr17 81195210 24937642 0.3071319354922538 0.848125655107405 chr18 78077248 23818926 0.305068718610574 1.109933332411322 chr19 59128983 15968879 0.27006855504347166 0.9072707253299569 chr20 63025520 21824208 0.3462757308468062 0.9244621083346891 chr21 48129895 12098292 0.25136751285245895 1.2357925686158913 chr22 51304566 11648077 0.2270378234950862 0.7072901210274103 chrMT 16571 245233 14.798925834288818 17.30868325060296 chrX 155270560 49817106 0.32084064100754195 0.851016328351888 chrY 59373566 1610968 0.027132747930282645 0.9843906599535598