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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,833,604 G→A 46.8% S116N (AGC→AAC) ‡ ygbL → predicted class II aldolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,833,6040GA46.8% 8.7 / 65.9 79S116N (AGC→AAC) ‡ygbLpredicted class II aldolase
Reads supporting (aligned to +/- strand):  ref base G (28/14);  new base A (14/23);  total (42/37)
Fisher's exact test for biased strand distribution p-value = 1.35e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

GCATTTGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATGGGAAATGTCCCGCTGGTGC  >  minE/1833548‑1833666
                                                        |                                                              
gCATTTGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCg                                                    >  1:1164086/1‑69 (MQ=255)
gCATTTGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCg                                                    >  1:2952565/1‑69 (MQ=255)
gCATTTGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCg                                                    >  1:812439/1‑69 (MQ=255)
 cATTTGCACAGCACATGGTCGCCGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGt                                                   >  1:2636582/1‑69 (MQ=255)
 cATTTGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGt                                                   >  1:2569153/1‑69 (MQ=255)
 cATTTGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGt                                                   >  1:1845958/1‑69 (MQ=255)
   tttGCACAGCTCATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTc                                                  <  1:2962585/68‑1 (MQ=255)
   tttGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTc                                                  <  1:2468656/68‑1 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGtt                                                         >  1:818377/1‑59 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:3187310/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:2485871/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:1872370/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:2480582/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:2412061/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:231448/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:500979/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:3237513/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:2236570/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:2293553/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:347206/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:1740306/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:622045/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:2620063/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:2964227/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:875469/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:917567/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCg                                                >  1:94353/1‑68 (MQ=255)
     tGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAG‑AACGTTATTCGTCCGtt                                              >  1:574535/1‑69 (MQ=255)
       cacagcacaTGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGtt                                              <  1:424461/68‑1 (MQ=255)
       cacagcacaTGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGtt                                              <  1:509250/68‑1 (MQ=255)
            cacaTGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTc                                                  <  1:2892908/59‑1 (MQ=255)
                  gTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACgt                                  >  1:1957614/1‑69 (MQ=255)
                  gTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACg                                   >  1:2646170/1‑68 (MQ=255)
                    cGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGtt                                              <  1:3129939/55‑1 (MQ=255)
                     gACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACgtggt                               <  1:3262000/69‑1 (MQ=255)
                     gACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACgtggt                               <  1:3315265/69‑1 (MQ=255)
                     gACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACgtggt                               <  1:3375573/69‑1 (MQ=255)
                     gACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACgtggt                               <  1:1547313/69‑1 (MQ=255)
                     gACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACgtggt                               <  1:1164163/69‑1 (MQ=255)
                     gACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACgtggt                               <  1:705814/69‑1 (MQ=255)
                     gACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACgtggt                               <  1:694165/69‑1 (MQ=255)
                               tCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGtt                                              <  1:2906665/44‑1 (MQ=255)
                                    cctggATGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:3037899/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:2356289/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:2701986/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:703097/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:625190/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:3021804/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:3348477/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:3269779/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:1808342/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:1024304/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:1042625/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:1291244/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:1303097/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:1921900/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:20687/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:2223427/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:2227366/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:2310292/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:2487909/66‑1 (MQ=255)
                                    cctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:2680150/66‑1 (MQ=255)
                                     ctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:565849/65‑1 (MQ=255)
                                     ctggAAGGGCTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:2993796/65‑1 (MQ=255)
                                              cTGGACAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATggg                   <  1:3139358/56‑1 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTg   >  1:2012609/1‑68 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:1217105/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:2946377/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:1005487/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:1340701/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:1273327/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:1778365/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:3376086/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:2570212/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:1116314/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:3166675/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:2413124/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGATGGGTAATGTCCCGCTGGTGc  >  1:2920044/1‑69 (MQ=255)
                                                  aCAGCAATAACGTTATTCGGCCGTTCACACCATACGTGGTGATGCGGAT‑GGTAATGTCCCGCTGGTGc  >  1:1245140/1‑68 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACgt                                  <  1:3109926/36‑1 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACgt                                  <  1:113613/36‑1 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACgt                                  <  1:1243445/36‑1 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACgt                                  <  1:699993/36‑1 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACgt                                  <  1:1284490/36‑1 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACgt                                  <  1:1511492/36‑1 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACgt                                  <  1:404869/36‑1 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACgt                                  <  1:3212025/36‑1 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATGGGAAATGTCCCGCTGGTGc  >  1:515412/1‑68 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATGGGAAATGTCCCGCTGGTGc  >  1:1378116/1‑68 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATGGGAAATGTCCCGCTGGTGc  >  1:391886/1‑68 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATGGGAAATGTCCCGCTGGTGc  >  1:2803514/1‑68 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATGGGAAATGTCCCGCTGGTGc  >  1:2688603/1‑68 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATGGGAAATGTCCCGCTGGTGc  >  1:3083613/1‑68 (MQ=255)
                                                   cagcagCAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATGGGAAATGTCCCGCTGGTGc  >  1:2748745/1‑68 (MQ=255)
                                                        |                                                              
GCATTTGCACAGCACATGGTCGACGGCGCTTTCCTGCCTGCAAGGGCTGGACAGCAGCAACGTTATTCGTCCGTTCACACCATACGTGGTGATGCGGATGGGAAATGTCCCGCTGGTGC  >  minE/1833548‑1833666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A