Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F21 I0 R1 148 22.8 1772010 97.0% 1718849 61.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,371,273 Δ2 bp 100% intergenic (‑6/+299) dcuA ← / ← aspA C4‑dicarboxylate antiporter/aspartate ammonia‑lyase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,371,2730A.95.0% 69.9 / ‑1.2 20intergenic (‑6/+300)dcuA/aspAC4‑dicarboxylate antiporter/aspartate ammonia‑lyase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (9/10);  total (9/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.
*W3110S.gb4,371,2740A.95.0% 68.6 / ‑1.5 20intergenic (‑7/+299)dcuA/aspAC4‑dicarboxylate antiporter/aspartate ammonia‑lyase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base . (9/10);  minor base T (0/1);  total (9/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGTTACGGCGCAGCAGCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGAAAAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGTT  >  W3110S.gb/4371204‑4371334
                                                                     ||                                                            
ggTTACGGCGCAGCAGCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGaa                                                              <  1:1330283/71‑1 (MQ=255)
            gcagcTTCTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATa                                                <  1:197859/71‑1 (MQ=255)
                cTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCg                                            <  1:1126137/71‑1 (MQ=255)
                    tctgtctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCAt                                        >  1:315381/1‑71 (MQ=255)
                          tgatgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAAt                                  >  1:736733/1‑71 (MQ=255)
                            atgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATaa                                   <  1:676110/68‑1 (MQ=255)
                            atgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAAt                                  >  1:902333/1‑69 (MQ=255)
                            atgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATg                                 >  1:266262/1‑70 (MQ=255)
                            atgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATg                                 <  1:1017611/70‑1 (MQ=255)
                             tgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga                               <  1:1354425/71‑1 (MQ=255)
                                 ccAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGAt                                                 >  1:943524/1‑49 (MQ=255)
                                   aGATAGTCAAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGa                          >  1:1527230/1‑70 (MQ=255)
                                        gTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCg                     <  1:1305142/70‑1 (MQ=255)
                                        gTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGa                    <  1:356065/71‑1 (MQ=255)
                                        gTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGa                    <  1:462697/71‑1 (MQ=255)
                                               ccGCCAGCAACCTGCATGGC‑‑ATAAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGa              <  1:965463/70‑1 (MQ=255)
                                                         ccTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAAt                                  >  1:198348/1‑40 (MQ=37)
                                                         ccTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGAt                            <  1:784981/46‑1 (MQ=37)
                                                          cTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGtt  >  1:1314904/1‑71 (MQ=255)
                                                           tGCATGGCAG‑‑AAATAGCGGCGATACCCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGtt  >  1:724280/1‑70 (MQ=255)
                                                            gCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATaa                                   <  1:191309/36‑1 (MQ=25)
                                                                     ||                                                            
GGTTACGGCGCAGCAGCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGAAAAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGTT  >  W3110S.gb/4371204‑4371334

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A