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 1,892,496 G→A 29.5% A128A (GCC→GCT)  ygdL ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,892,4960GA29.5% 99.3 / 44.0 98A128A (GCC→GCT) ygdLconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (21/48);  new base A (16/13);  total (37/61)
Fisher's exact test for biased strand distribution p-value = 2.48e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.34e-01

GGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAAT  >  minE/1892438‑1892560
                                                          |                                                                
ggATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCatcaatca                                                        >  1:3049113/1‑69 (MQ=255)
ggATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCatcaatca                                                        <  1:3202177/69‑1 (MQ=255)
    tttATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCa                                                               >  1:3310092/1‑58 (MQ=255)
     ttATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCatcaat                                                          <  1:1853276/62‑1 (MQ=255)
          gcgcCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATa                                              <  1:255645/69‑1 (MQ=255)
          gcgcCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATa                                              <  1:368440/69‑1 (MQ=255)
          gcgcCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATa                                              <  1:1509953/69‑1 (MQ=255)
          gcgcCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATa                                              <  1:348319/69‑1 (MQ=255)
          gcgcCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATa                                              <  1:2147865/69‑1 (MQ=255)
          gcgcCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATa                                              <  1:31953/69‑1 (MQ=255)
          gcgcCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATa                                              <  1:2509078/69‑1 (MQ=255)
            gcCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATa                                              <  1:3224312/67‑1 (MQ=255)
                aCAATAATCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:289864/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCTATCACGTACGAATAAccggc                                        <  1:734911/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:1998173/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:2148333/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:1670868/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:36720/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:1637729/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:240985/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:525304/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:844724/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:2249903/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:1433836/69‑4 (MQ=255)
                aCAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAAccggc                                        <  1:1399031/69‑4 (MQ=255)
                   aTAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGGATCAATCACGTACGAATAACCCACGCt                                     <  1:2236747/69‑1 (MQ=255)
                     aaGCAATCAGCGCCGCTTTGGGCCGTACACTATCTATGGCATCAATCACGTACGAATAACCCACGCTCa                                   <  1:573193/69‑1 (MQ=255)
                     aaGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGTCATCAATCACGTACGAATAACCCACGCTCa                                   <  1:1758045/69‑1 (MQ=255)
                     aaGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCa                                   <  1:2104891/69‑1 (MQ=255)
                     aaGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCa                                   <  1:1248598/69‑1 (MQ=255)
                     aaGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCa                                   <  1:659626/69‑1 (MQ=255)
                     aaGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCa                                   <  1:1768013/69‑1 (MQ=255)
                     aaGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCa                                   <  1:655626/69‑1 (MQ=255)
                     aaGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCa                                   <  1:1678993/69‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:2343568/68‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:2968900/68‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:300052/68‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:259628/68‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:1965106/68‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:1612959/68‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:1374944/68‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:819886/68‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:870651/68‑1 (MQ=255)
                        cAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 <  1:1018181/68‑1 (MQ=255)
                           tCAGCGCCGCTTTGGGCCGTACACTATCAATAGCATCAATCACGTAc                                                   >  1:23748/1‑47 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTa                  >  1:903753/1‑68 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:356237/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:304234/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:3027132/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:475825/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:801414/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:850571/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:975794/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:2656475/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:1035403/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:1118541/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:1153281/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:1660116/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTCATATATTGCGCTACGTTAt                 >  1:1901931/1‑69 (MQ=255)
                                       tGGGCCGTACACTATCAATAGCATCAATCACGTACGAATAACCGGCATTAATATATTGCGCTAAGTTAt                 >  1:1656744/1‑69 (MQ=255)
                                                cacTATCAATGGCATGAATCACGTACGAATAACCCACGCTCata                                 >  1:787527/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:2689596/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:1171644/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:1246676/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:750062/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:1594199/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:565897/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:1663474/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:3359827/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:2796933/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:19986/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCata                                 >  1:2206933/1‑44 (MQ=255)
                                                cacTATCAATGGCATCAATCACGTACGAATAACCCACGCTCa                                   >  1:902145/1‑42 (MQ=255)
                                                    aTCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGaa    >  1:3304409/1‑69 (MQ=255)
                                                    aTCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGaa    >  1:380620/1‑69 (MQ=255)
                                                    aTCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGaa    >  1:2207303/1‑69 (MQ=255)
                                                    aTCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGaa    >  1:1431338/1‑69 (MQ=255)
                                                    aTCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGaa    >  1:2196954/1‑69 (MQ=255)
                                                    aTCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGaa    >  1:1506033/1‑69 (MQ=255)
                                                     tCAATGGCATCAATCACGTACGAATAACCCACGCt                                     <  1:1828537/35‑1 (MQ=255)
                                                     tCAATGGCATCAATCACGTACGAATAACCCACGCt                                     <  1:2855868/35‑1 (MQ=255)
                                                     tCAATGGCATCAATCACGTACGAATAACCCACGCt                                     <  1:821252/35‑1 (MQ=255)
                                                     tCAATGGCATCAATCACGTACGAATAACCCACGCt                                     <  1:1254726/35‑1 (MQ=255)
                                                     tCAATGGCATCAATCACGTACGAATAACCCACGCt                                     <  1:1711110/35‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:657385/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:2096338/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:1351755/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:1617599/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:2001870/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:428738/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:2988556/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:407358/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:2405498/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:2521080/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:1128224/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:380881/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:920655/68‑1 (MQ=255)
                                                       aaTGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAat  <  1:1896458/68‑1 (MQ=255)
                                                          |                                                                
GGATTTTATTGCGCCGACAATAAGCAATCAGCGCCGCTTTGGGCCGTACACTATCAATGGCATCAATCACGTACGAATAACCCACGCTCATATACTGCGCTACGTTATCCGGCGTCACGAAAT  >  minE/1892438‑1892560

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