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 1,971,940 C→A 39.5% S322S (TCG→TCT)  speA ← biosynthetic arginine decarboxylase, PLP‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,971,9400CA39.5% 67.1 / 76.2 91S322S (TCG→TCT) speAbiosynthetic arginine decarboxylase, PLP‑binding
Reads supporting (aligned to +/- strand):  ref base C (17/38);  new base A (19/17);  total (36/55)
Fisher's exact test for biased strand distribution p-value = 4.90e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01

CCAATCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGAATATTGACGCC  >  minE/1971875‑1972005
                                                                 |                                                                 
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:902332/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:2639000/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:230099/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:2784022/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:3010784/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:1923788/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:3113155/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:3331415/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:1695219/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:3423026/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:370606/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:380015/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:389537/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:1196652/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:473729/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:529345/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:1229318/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:68579/1‑69 (MQ=255)
ccAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTACGGAGCAGTCAGACTGAGaa                                                                >  1:782268/1‑69 (MQ=255)
  aaTCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACg                                                              <  1:1523618/69‑1 (MQ=255)
  aaTCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACg                                                              <  1:2124176/69‑1 (MQ=255)
     cGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGt                                                           >  1:3208619/1‑69 (MQ=255)
     cGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGt                                                           >  1:2364673/1‑69 (MQ=255)
              aaTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATa                                                  <  1:2487157/69‑1 (MQ=255)
              aaTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATa                                                  <  1:2483269/69‑1 (MQ=255)
               aTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATaa                                                 <  1:1300562/69‑1 (MQ=255)
               aTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATaa                                                 <  1:3107842/69‑1 (MQ=255)
               aTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATaa                                                 <  1:2054038/69‑1 (MQ=255)
               aTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATaa                                                 <  1:420101/69‑1 (MQ=255)
               aTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATaa                                                 <  1:2939213/69‑1 (MQ=255)
               aTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATaa                                                 <  1:283719/69‑1 (MQ=255)
               aTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATaa                                                 <  1:853436/69‑1 (MQ=255)
               aTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATa                                                  <  1:419807/68‑1 (MQ=255)
               aTGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATa                                                  <  1:2373790/68‑1 (MQ=255)
                 gttgttGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATc                                               >  1:622461/1‑69 (MQ=255)
                 gttgttGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATc                                               >  1:967167/1‑69 (MQ=255)
                 gttgttGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATc                                               >  1:2524258/1‑69 (MQ=255)
                 gttgttGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATc                                               >  1:2045850/1‑69 (MQ=255)
                  ttgttgGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCTGACTGCTAACGAGTACCTTCATaa                                                 <  1:2907334/66‑1 (MQ=255)
                    gttgGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCa                                             <  1:3241055/68‑1 (MQ=255)
                    gttgGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCa                                             <  1:403994/68‑1 (MQ=255)
                    gttgGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCa                                             <  1:3430517/68‑1 (MQ=255)
                    gttgGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCa                                             <  1:2688682/68‑1 (MQ=255)
                            aTTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAc                                    <  1:1679931/69‑1 (MQ=255)
                                   gAGGCCGTAGTTCACCGAACAGTCGGACTGCTAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:217942/69‑1 (MQ=255)
                                   gAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:2667815/69‑1 (MQ=255)
                                   gAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:2111334/69‑1 (MQ=255)
                                   gAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:3354413/69‑1 (MQ=255)
                                   gAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:4162/69‑1 (MQ=255)
                                   gAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:1514907/69‑1 (MQ=255)
                                   gAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:121414/69‑1 (MQ=255)
                                   gAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:2430607/69‑1 (MQ=255)
                                            gTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGa                     >  1:1087814/1‑68 (MQ=255)
                                            gTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGa                     >  1:1183401/1‑68 (MQ=255)
                                            gTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGa                     >  1:927662/1‑68 (MQ=255)
                                            gTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGa                     >  1:2475707/1‑68 (MQ=255)
                                            gTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGa                     >  1:2278498/1‑68 (MQ=255)
                                            gTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACAGCCGCCGACGTCGa                     >  1:1796948/1‑68 (MQ=255)
                                               cACCGAACAGTCGGACTGCGAACGAGTAGCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCa                 >  1:1649022/1‑69 (MQ=255)
                                               cACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             >  1:2519722/1‑57 (MQ=255)
                                               cACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             >  1:1460357/1‑57 (MQ=255)
                                               cACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             >  1:515480/1‑57 (MQ=255)
                                               cACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCa                 >  1:2626575/1‑69 (MQ=255)
                                               cACCGAACAGGCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:1597310/57‑1 (MQ=255)
                                                aCCGAACAGTCTGACTGCGAACGAGTACCTTCATa                                                  <  1:370074/35‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:1375786/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:531889/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:1458448/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:2618990/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:854288/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:856614/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:2578519/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:1527328/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:2637931/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:3027568/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:1830043/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:3002854/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:3262574/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:335122/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:2245832/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:1653784/65‑1 (MQ=255)
                                                   gagcAGTCAGACTGAGAACGGGTGCCTTCATAGTCCACGCCCAGACCGCCGCCGACGTCGAAGCACTg              <  1:2406956/65‑1 (MQ=255)
                                                    aaCAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGaa            <  1:1393149/69‑1 (MQ=255)
                                                    aaCAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGaa            <  1:688541/69‑1 (MQ=255)
                                                    aaCAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGaa            <  1:836408/69‑1 (MQ=255)
                                                    aaCAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGaa            <  1:1760149/69‑1 (MQ=255)
                                                    aaCAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGaa            <  1:2539935/69‑1 (MQ=255)
                                                        gTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGAATAtt        <  1:1428845/69‑1 (MQ=255)
                                                        gTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGAATAtt        <  1:62339/69‑1 (MQ=255)
                                                            gACTGCGAACGAGTACCTTCATAATCCACGCCCAGAccgccgcc                             <  1:3086174/44‑1 (MQ=255)
                                                              cTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGAATATTGACGcc  <  1:2837928/69‑1 (MQ=255)
                                                                 |                                                                 
CCAATCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGTCGGACTGCGAACGAGTACCTTCATAATCCACGCCCAGACCGCCGCCGACGTCGAAGCACTGAATATTGACGCC  >  minE/1971875‑1972005

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