BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3085105.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 = 1,144,071
number of mapped reads = 858,375 (75.03%)
number of supplementary alignments = 5,376 (0.47%)
number of secondary alignments = 0
number of mapped bases = 53,597,610 bp
number of sequenced bases = 53,578,679 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 16,459
duplication rate = 1.47%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.9667
>>>>>>> ACTG content
number of A's = 16,010,251 bp (29.88%)
number of C's = 10,468,102 bp (19.54%)
number of T's = 15,457,543 bp (28.85%)
number of G's = 11,641,636 bp (21.73%)
number of N's = 1,147 bp (0%)
GC percentage = 41.27%
>>>>>>> Mismatches and indels
general error rate = 0.0097
number of mismatches = 510,959
number of insertions = 4,470
mapped reads with insertion percentage = 0.52%
number of deletions = 11,561
mapped reads with deletion percentage = 1.33%
homopolymer indels = 43.96%
>>>>>>> Coverage
mean coverageData = 0.0173X
std coverageData = 0.1763X
There is a 1.62% of reference with a coverageData >= 1X
There is a 0.08% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% 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 4603090 0.018467717278024355 0.238461990922982
chr2 243199373 5105336 0.02099238964732035 0.2090332463530585
chr3 198022430 3375213 0.017044599442598497 0.13966442964710454
chr4 191154276 3697774 0.019344448250794035 0.14805118830775305
chr5 180915260 2410890 0.013326073212397893 0.12029757965478889
chr6 171115067 3730020 0.021798314230271728 0.1713523893152751
chr7 159138663 4259738 0.026767461279978203 0.1930857893502755
chr8 146364022 3530278 0.02411984825068554 0.2669251267136415
chr9 141213431 1555004 0.01101172876395872 0.14473438580476644
chr10 135534747 3606160 0.02660690398455534 0.26193786964178883
chr11 135006516 2657961 0.019687649742772415 0.19876355988506517
chr12 133851895 2396501 0.01790412455497922 0.14068304681571037
chr13 115169878 1173809 0.010191979190947827 0.10450273599481955
chr14 107349540 1733642 0.016149505624337094 0.13545606199157012
chr15 102531392 1080214 0.010535446548896947 0.10634369087537238
chr16 90354753 1295440 0.014337264581975007 0.13444300595157335
chr17 81195210 679200 0.008365025473793343 0.10957915320393356
chr18 78077248 1498937 0.019198127987297912 0.2456919410708823
chr19 59128983 589154 0.009963878458724717 0.16286178843715296
chr20 63025520 1251614 0.019858844480775406 0.14885462071262429
chr21 48129895 685157 0.014235580609515146 0.12959427841841184
chr22 51304566 378399 0.007375542364007133 0.08884400193581576
chrMT 16571 58683 3.541307102769899 2.640949041538319
chrX 155270560 2111522 0.01359898489449642 0.13072882728653587
chrY 59373566 133874 0.0022547744563632915 0.060080176073576116