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 1,325,808 A→G 23.8% S401S (AGT→AGC) ‡ wcaK ← predicted pyruvyl transferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,325,8080AG23.8% 86.8 / 22.4 71S401S (AGT→AGC) ‡wcaKpredicted pyruvyl transferase
Reads supporting (aligned to +/- strand):  ref base A (28/26);  new base G (9/8);  total (37/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

TGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTGCA  >  minE/1325773‑1325866
                                   |                                                          
tGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCa                                                >  1:3065589/1‑48 (MQ=255)
tGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCa                                                >  1:2757351/1‑48 (MQ=255)
tGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCa                                                >  1:2455628/1‑48 (MQ=255)
tGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCa                                                >  1:2038858/1‑48 (MQ=255)
tGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCa                                                >  1:1681624/1‑48 (MQ=255)
tGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCa                                                >  1:1809017/1‑48 (MQ=255)
tGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCa                                                >  1:1804963/1‑48 (MQ=255)
  cATTCCCGTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTaa                         >  1:1029790/1‑69 (MQ=255)
  cATTCCCGTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTaa                         >  1:2850444/1‑69 (MQ=255)
  cATTCCCGTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTaa                         >  1:2812535/1‑69 (MQ=255)
  cATTCCCGTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTaa                         >  1:3279818/1‑69 (MQ=255)
  cATTCCCGTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTaa                         >  1:3408956/1‑69 (MQ=255)
  cATTCCCGTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTaa                         >  1:219926/1‑69 (MQ=255)
  cATTCCCGTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTaa                         >  1:1876401/1‑69 (MQ=255)
  cATTCCCGTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTaa                         >  1:706214/1‑69 (MQ=255)
  cATTCCCGTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTaa                         >  1:1127694/1‑69 (MQ=255)
    ttCCTGTCTGACGCTCACTACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCt                           <  1:2404167/65‑1 (MQ=255)
      ccTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTa                     <  1:1925704/69‑1 (MQ=255)
      ccTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTa                     >  1:3178922/1‑69 (MQ=255)
      ccTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTa                     <  1:859209/69‑1 (MQ=255)
      ccTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTa                     >  1:3304678/1‑69 (MQ=255)
      ccTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGACGGAAGCTGGCCTAAGGTa                     >  1:1520830/1‑69 (MQ=255)
         gTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTAAGGTAccc                  <  1:182495/69‑1 (MQ=255)
         gTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTAAGGTATcc                  <  1:2260783/69‑1 (MQ=255)
         gTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTAAGGTATcc                  <  1:2890764/69‑1 (MQ=255)
         gTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTAAGGTATcc                  <  1:2504157/69‑1 (MQ=255)
         gTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTAAGGTATcc                  <  1:3016424/69‑1 (MQ=255)
         gTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTAAGGTATcc                  <  1:571624/69‑1 (MQ=255)
         gTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTAAGGTATcc                  <  1:58148/69‑1 (MQ=255)
         gTCTGACGTTCGCGACTGACAGCTTCGTTAAGTCGTGCGTTCAGCGCCGGAAGCTGGCCTAAGGTATcc                  <  1:929719/69‑1 (MQ=255)
           cTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTTGCCTAAGGTATCCGc                >  1:1351866/1‑69 (MQ=255)
           cTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                >  1:2383085/1‑69 (MQ=255)
           cTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                >  1:2690655/1‑69 (MQ=255)
           cTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                >  1:1301265/1‑69 (MQ=255)
           cTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                >  1:439813/1‑69 (MQ=255)
           cTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                >  1:320986/1‑69 (MQ=255)
            tGACGCTCACGACTTACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                <  1:1974217/68‑1 (MQ=255)
            tGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                <  1:304324/68‑1 (MQ=255)
            tGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                <  1:645918/68‑1 (MQ=255)
            tGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                <  1:1177218/68‑1 (MQ=255)
            tGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                <  1:3383041/68‑1 (MQ=255)
            tGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                <  1:3394256/68‑1 (MQ=255)
            tGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                <  1:610278/68‑1 (MQ=255)
            tGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc                <  1:642028/68‑1 (MQ=255)
                gCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAAcc            <  1:343588/68‑1 (MQ=255)
                gCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAAcc            <  1:896967/68‑1 (MQ=255)
                gCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAAcc            <  1:937258/68‑1 (MQ=255)
                gCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAAcc            <  1:227244/68‑1 (MQ=255)
                ccTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAAcc            <  1:245203/67‑1 (MQ=255)
                 cTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCAt          <  1:1250490/69‑1 (MQ=255)
                 cTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCAt          <  1:2702942/69‑1 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:2607373/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:2534953/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:2478419/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:2792434/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:3179805/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:1987622/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:634031/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:1777824/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:1777696/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:69348/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:1663880/1‑69 (MQ=255)
                   cACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCg        >  1:1379696/1‑69 (MQ=255)
                       aCTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTg    <  1:882277/69‑1 (MQ=255)
                        cTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTg    <  1:2702791/68‑1 (MQ=255)
                         tGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTGCa  <  1:1002307/69‑1 (MQ=255)
                         tGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTGCa  <  1:3184871/69‑1 (MQ=255)
                         tGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTGCa  <  1:932546/69‑1 (MQ=255)
                         tGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTGCa  <  1:136864/69‑1 (MQ=255)
                         tGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTGCa  <  1:1944178/69‑1 (MQ=255)
                         tGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTGCa  <  1:3290615/69‑1 (MQ=255)
                                   |                                                          
TGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCATCGCTTGCA  >  minE/1325773‑1325866

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