BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006394.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 = 13,051,058 number of mapped reads = 11,569,884 (88.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,864,357 number of mapped paired reads (second in pair) = 5,705,527 number of mapped paired reads (both in pair) = 10,623,576 number of mapped paired reads (singletons) = 946,308 number of mapped bases = 448,057,341 bp number of sequenced bases = 448,002,412 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 772,330 duplication rate = 5.93% >>>>>>> Insert size mean insert size = 72,831.9263 std insert size = 2,573,582.0288 median insert size = 134 >>>>>>> Mapping quality mean mapping quality = 48.3166 >>>>>>> ACTG content number of A's = 125,508,469 bp (28.02%) number of C's = 96,027,720 bp (21.43%) number of T's = 127,041,548 bp (28.36%) number of G's = 99,405,799 bp (22.19%) number of N's = 18,876 bp (0%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 1,644,085 number of insertions = 11,660 mapped reads with insertion percentage = 0.1% number of deletions = 41,015 mapped reads with deletion percentage = 0.35% homopolymer indels = 43.95% >>>>>>> Coverage mean coverageData = 0.1447X std coverageData = 0.7489X There is a 10.87% of reference with a coverageData >= 1X There is a 2.47% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% 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 37573572 0.15074615200256614 1.1144175672104373 chr2 243199373 38293858 0.15745870364558875 0.6503566193624896 chr3 198022430 29875126 0.1508673840635124 0.4835389817305722 chr4 191154276 28646810 0.14986225053108412 0.5537332978842195 chr5 180915260 27079635 0.1496813204148727 0.48215982383442285 chr6 171115067 25541884 0.1492672997638484 0.5590715638041872 chr7 159138663 24699488 0.15520733638437065 0.9293834833221901 chr8 146364022 22573253 0.15422678805587892 1.7606583922382013 chr9 141213431 18022371 0.12762504864002633 0.541956681811343 chr10 135534747 21130965 0.15590810082081755 0.743071649356092 chr11 135006516 20272857 0.15016206328885637 0.6315717831709634 chr12 133851895 20099103 0.15015927118551442 0.4907271575591263 chr13 115169878 13919339 0.12085919722863647 0.430365022394313 chr14 107349540 13289037 0.12379221187161119 0.49992391113326895 chr15 102531392 12959262 0.126393114803318 0.44304302498608816 chr16 90354753 13467471 0.14905105213446823 0.6087905341184512 chr17 81195210 12403031 0.1527556982733341 0.527378273923059 chr18 78077248 11388671 0.14586414469936235 0.9265829045544688 chr19 59128983 9208820 0.1557412208493422 0.810115228924067 chr20 63025520 10010450 0.15883169230495836 0.5364106550816936 chr21 48129895 5859731 0.12174826061847839 0.5081897392701898 chr22 51304566 5590025 0.10895765105975168 0.42480853066021224 chrMT 16571 2834 0.17102166435338845 0.62375696693517 chrX 155270560 25097245 0.1616355669741901 0.5585140121133023 chrY 59373566 1052503 0.017726794445865016 0.409581722926413