BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081029.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,390,197 number of mapped reads = 2,619,616 (77.27%) number of supplementary alignments = 11,951 (0.35%) number of secondary alignments = 0 number of mapped bases = 164,196,239 bp number of sequenced bases = 164,138,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,254 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4201 >>>>>>> ACTG content number of A's = 46,360,361 bp (28.24%) number of C's = 33,105,603 bp (20.17%) number of T's = 47,939,781 bp (29.21%) number of G's = 36,731,175 bp (22.38%) number of N's = 2,071 bp (0%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,242,573 number of insertions = 10,895 mapped reads with insertion percentage = 0.41% number of deletions = 32,792 mapped reads with deletion percentage = 1.24% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.3611X There is a 4.45% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 14245755 0.057154341051772146 0.6243401023244146 chr2 243199373 14065031 0.057833335779200384 0.39571221328095363 chr3 198022430 11107268 0.05609095898883778 0.2719380031667577 chr4 191154276 9721605 0.050857376583090405 0.2709131101858015 chr5 180915260 10121736 0.05594738663836318 0.2751354914267687 chr6 171115067 9387896 0.05486305890293109 0.3492357226319451 chr7 159138663 7872548 0.049469738224456494 0.38428597706993656 chr8 146364022 8437142 0.0576449176833908 0.377918159612499 chr9 141213431 6370728 0.04511417897636097 0.3270083227597457 chr10 135534747 7602951 0.05609595449349974 0.35205893174906333 chr11 135006516 7028139 0.052057776233556015 0.3248538033396311 chr12 133851895 7957820 0.05945242687822985 0.2838698117248795 chr13 115169878 5441681 0.047249168745320716 0.25018540939107425 chr14 107349540 5255337 0.0489553751231724 0.2691236928694238 chr15 102531392 4578737 0.044656928094763404 0.26113007226638446 chr16 90354753 4875673 0.05396144461819291 0.2859934740079843 chr17 81195210 4602258 0.05668139783122674 0.29032409142683574 chr18 78077248 4333750 0.05550592664331612 0.5905368586695613 chr19 59128983 3527795 0.05966270382157596 0.4693200131771573 chr20 63025520 3540400 0.056174070440037624 0.2782028366729465 chr21 48129895 1794893 0.03729268472328892 0.23329559794291102 chr22 51304566 2071260 0.040371845266169874 0.2306315859045396 chrMT 16571 53132 3.2063243014905556 2.574849316314812 chrX 155270560 9824210 0.0632715564367128 0.31818623459033885 chrY 59373566 378494 0.006374789750711621 0.12253908450717382