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 460,885 A→G 28.0% D13D (GAT→GAC)  gltA ← citrate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE460,8850AG28.0% 92.1 / 37.5 89D13D (GAT→GAC) gltAcitrate synthase
Reads supporting (aligned to +/- strand):  ref base A (15/49);  new base G (11/14);  total (26/63)
Fisher's exact test for biased strand distribution p-value = 7.11e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.03e-01

AACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTA  >  minE/460837‑460945
                                                |                                                            
aaCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGttt                                          >  1:309256/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:699732/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:603745/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:3423115/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:3152591/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:308764/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:1082298/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:2536603/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:2442409/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:169970/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:1682944/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:1649930/1‑69 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGttt                                          >  1:1682808/1‑68 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtt                                           >  1:1842566/1‑67 (MQ=255)
 aCATCTTGACCCAGCGTGCCTTTAAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGtttt                                         >  1:1021463/1‑69 (MQ=255)
          cccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGt                                 <  1:3377899/68‑1 (MQ=255)
          cccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGt                                 <  1:240907/68‑1 (MQ=255)
           ccAGCGTGCCTTTCCGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:1913535/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:1997873/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:1252229/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:632119/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:2506828/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:105883/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:2823052/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:519702/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:88926/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:3133958/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:1483745/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:3345494/69‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGtt                                <  1:1622163/68‑2 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTa                                <  1:2192310/68‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTa                                <  1:999359/68‑1 (MQ=255)
           ccAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTa                                <  1:884372/68‑1 (MQ=255)
            cAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:2871848/68‑1 (MQ=255)
            cAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCTTTTGTAt                               <  1:1664685/68‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:1003849/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:1475489/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:3336423/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:3273435/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:3188759/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:1061123/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:1065334/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:376385/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:1078680/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:1352900/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:2596121/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:255967/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:607900/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:752375/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:2466572/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:1240902/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:2080563/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:2148163/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:781181/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:2314635/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:2216491/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:753900/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:2170324/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:683317/69‑1 (MQ=255)
               cGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:218723/69‑1 (MQ=255)
                gTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGc                           <  1:1183965/68‑1 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:992792/1‑46 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:858207/1‑46 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:590862/1‑46 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:859679/1‑46 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:2708074/1‑46 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:1392066/1‑46 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:1387198/1‑46 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:1438267/1‑46 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:1348090/1‑46 (MQ=255)
                              aTCCAGTTCAACAGCTGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:170002/1‑46 (MQ=255)
                              aTCCAGTTCAACAGATGTGTCCCCGTTGAGGGTGAGTTTTGCtttt                                   >  1:1857404/1‑46 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:2079850/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:1452494/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:1544661/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:875233/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:1915192/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:744986/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:3186222/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:2187990/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:2438550/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:2534774/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:2602231/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:2865587/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:51872/68‑1 (MQ=255)
                                        aCAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCtt   <  1:3426096/68‑1 (MQ=255)
                                         cAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTa  <  1:1768659/68‑1 (MQ=255)
                                         cAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTa  <  1:491635/68‑1 (MQ=255)
                                         cAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTa  <  1:1069148/68‑1 (MQ=255)
                                                |                                                            
AACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTA  >  minE/460837‑460945

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A