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 508,902 C→T 44.5% T187T (ACC→ACT)  ybhI → predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE508,9020CT44.5% 27.1 / 78.9 101T187T (ACC→ACT) ybhIpredicted transporter
Reads supporting (aligned to +/- strand):  ref base C (40/16);  new base T (13/32);  total (53/48)
Fisher's exact test for biased strand distribution p-value = 2.45e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.88e-01

Only 100 of 101 total aligned reads displayed.

TCCGAACCGGAAAAAAGTCCGCGTCGTGTCGGACATTACCTGATGATGTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATC  >  minE/508837‑508965
                                                                 |                                                               
tCCGAACCGGAAAAAAGTCCGCGTCGTGTCGGACATTACCTGATGATGTCCATTTACATGGTCACCaaa                                                              >  1:3294534/1‑69 (MQ=255)
tCCGAACCGGAAAAAAGTCCGCGTCGTGTCGGACATTACCTGATGATGTCCATTTACATGGTCACCaaa                                                              >  1:3204393/1‑69 (MQ=255)
    aaCCGGAAAAAAGTCCGCGTCGTGTCGGACATTACCTGATGATGTCCATTTACATTGTCACCAAAacca                                                          <  1:2892179/69‑1 (MQ=255)
    aaCCGGAAAAAAGTCCGCGTCGTGTCGGACATTACCTGATGATGTCCATTTACATGGTCACCAAAacca                                                          <  1:1374284/69‑1 (MQ=255)
      ccGGAAAAAAGTCCGCGTCGTGTTGGACATTACCTGATGATGTCCATTTACATGGTCACTAAAagcacc                                                        <  1:3360509/69‑1 (MQ=255)
      ccGGAAAAAAGTCCGCGTCGTGTTGGACATTACCTGATGATGTCCATTTACATGGTCACTAAAaccacc                                                        <  1:1094398/69‑1 (MQ=255)
      ccGGAAAAAAGTCCGCGTCGTGTTGGACATTACCTGATGATGTCCATTTACATGGTCACTAAAaccacc                                                        <  1:2075662/69‑1 (MQ=255)
      ccGGAAAAAAGTCCGCGTCGTGTTGGACATTACCTGATGATGTCCATTTACATGGTCACTAAAaccacc                                                        <  1:542950/69‑1 (MQ=255)
      ccGGAAAAAAGTCCGCGTCGTGTTGGACATTACCTGATGATGTCCATTTACATGGTCACTAAAaccacc                                                        <  1:118558/69‑1 (MQ=255)
      ccGGAAAAAAGTCCGCGTCGTGTTGGACATTACCTGATGATGTCCATTTACATGGTCACTAAAaccacc                                                        <  1:1455927/69‑1 (MQ=255)
      ccGGAAAAAAGTCCGCGTCGTGTTGGACATTACCTGATGATGTCCATTTACATGGTCACTAAAaccacc                                                        <  1:1454144/69‑1 (MQ=255)
       cGGAAAAAAGTCCGCGTCGTGTTGGACATTACCTGATGATGTCCATTTACATGGTCACTAAAaccacc                                                        <  1:3065913/68‑1 (MQ=255)
       cGGAAAAAAGTCCGCGTCGTGTTGGACATTACCTGATGATGTCCATTTACATGGTCACTAAAaccacc                                                        <  1:1836376/68‑1 (MQ=255)
                           gtCGGACATTACCTGATGATGTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:524095/68‑1 (MQ=255)
                           gtCGGACATTACCTGATGATGTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:3281689/68‑1 (MQ=255)
                            tCGGACATTACCTGATGATGTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:1880075/67‑1 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:2666387/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:531435/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:1967422/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:2637196/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:252116/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:2081310/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:616598/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:1008170/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:1118539/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:3098486/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:3410478/1‑69 (MQ=255)
                                       cTGATGATGTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAAc                       >  1:535327/1‑69 (MQ=255)
                                            gatgTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  <  1:2660110/69‑1 (MQ=255)
                                            gatgTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  <  1:2031765/69‑1 (MQ=255)
                                            gatgTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  <  1:323494/69‑1 (MQ=255)
                                            gatgTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  <  1:1471532/69‑1 (MQ=255)
                                            gatgTCCATTTACATGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  <  1:3201469/69‑1 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCtata                                                 >  1:3392609/1‑38 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTc                   >  1:2001315/1‑68 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTc                   >  1:2970657/1‑68 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  >  1:620519/1‑69 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  >  1:3429313/1‑69 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  >  1:2898429/1‑69 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  >  1:3432989/1‑69 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  >  1:875031/1‑69 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  >  1:1448626/1‑69 (MQ=255)
                                            gatgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCt                  >  1:1420519/1‑69 (MQ=255)
                                             atgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCgggg                          >  1:1070383/1‑60 (MQ=255)
                                             atgTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCgggg                          >  1:3354459/1‑60 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTTTATGTTCTTTACCGc                                    <  1:1311697/47‑1 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    >  1:759564/1‑47 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:1561854/47‑1 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:14502/47‑1 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:693459/47‑1 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:1677395/47‑1 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:1949185/47‑1 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:3311584/47‑1 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:2053518/47‑1 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:579116/47‑1 (MQ=255)
                                                tCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:853306/47‑1 (MQ=255)
                                                     ttACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGc                                    <  1:3287923/42‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:1365571/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:332997/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:3240171/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:1268379/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:412746/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:1496629/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:1633464/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:2199737/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:2962083/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:1700358/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:1828984/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:2755061/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:2219307/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:2724139/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:1561764/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:2455616/68‑1 (MQ=255)
                                                         aTGGTCACTAAAACCACCAGCTATATGTTCTTTACCGAAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:651760/68‑1 (MQ=255)
                                                          tGGTCACTAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAAt      <  1:211823/67‑1 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:651786/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:879296/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:611234/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:599278/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:56993/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:909683/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:2279999/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:103413/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:1120814/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:1246057/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:1293850/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:1503888/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:1673307/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:1949351/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:1978131/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:460956/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:2359719/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:236144/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:2492614/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:2728114/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:2755290/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:3068135/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:3185961/1‑69 (MQ=255)
                                                            gTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:3288347/1‑69 (MQ=255)
                                                            gTCACCAAAACAACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATc  >  1:2166385/1‑69 (MQ=255)
                                                                 |                                                               
TCCGAACCGGAAAAAAGTCCGCGTCGTGTCGGACATTACCTGATGATGTCCATTTACATGGTCACCAAAACCACCAGCTATATGTTCTTTACCGCAATGGCGGGGAACATTCTGGCGCTGAAAATGATC  >  minE/508837‑508965

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