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
A21 F5 I0 R1 24 41.2 1474486 89.7% 1322613 148.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_pae_tpiA 4,604,632 C→A 100% A186E (GCA→GAA)  bglJ → bgl operon transcriptional activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA4,604,6320CA93.9% 122.7 / 0.1 48A186E (GCA→GAA) bglJbgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (1/2);  new base A (26/19);  total (27/21)
Fisher's exact test for biased strand distribution p-value = 5.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.70e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_pae_tpiA/4604491‑4604777
                                                                                                                                             |                                                                                                                                                 
accgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTGCGAGAGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATaaa                                                                                                                                            <  1:57484/149‑1 (MQ=255)
       gAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCACCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAtg                                                                                                                                     >  2:650174/1‑149 (MQ=255)
        aaCAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTGTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCGATATCACAACAATCCGTGAACATAAATTACAtgt                                                                                                                                    >  1:155444/1‑149 (MQ=255)
              cAGTGGAACAAAAACCAAAGCCGGACGTAAAGCCCGACGGAGAGAGAAATATTGCACTTTAGGTCGCGTGGCTACGCAATGACACAAATTGCCGAGCAGCTTAAACGCAATAACAAAACGATCCGTGAACATAAATTTAATGTGATGTc                                                                                                                              <  1:243154/149‑1 (MQ=255)
                 tGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGaa                                                                                                                           >  1:123216/1‑149 (MQ=255)
                   gTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAAc                                                                                                                         >  1:409044/1‑149 (MQ=255)
                    tACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACt                                                                                                                        >  1:53122/1‑149 (MQ=255)
                        ttAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGCTCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGc                                                                                                                    <  2:338554/149‑1 (MQ=255)
                          aaCCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGt                                                                                                                  <  1:410740/149‑1 (MQ=255)
                             cAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAg                                                                                                               >  1:367810/1‑149 (MQ=255)
                              aaaGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGt                                                                                                              >  1:101434/1‑149 (MQ=255)
                               aaGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACCCAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCAGTGAACATCAATTTAAAGTGATCTCGGAAGTGGACATCAttt                                                                                                             >  2:203499/1‑149 (MQ=255)
                                  ccGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTg                                                                                                          >  2:220139/1‑149 (MQ=255)
                                    ggACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTAGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATCTCAAAACGATCCGTGAACATAAATTTAATGTGATATCGAAACTGGGCGTCAGTTCTGAc                                                                                                        >  1:366355/1‑149 (MQ=255)
                                        gTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAg                                                                                                    <  1:365176/149‑1 (MQ=255)
                                                cGACGGAGAGAGAAATATTGCGCTTTAGGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGttgttg                                                                                            <  1:29994/149‑1 (MQ=255)
                                                 gACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTgg                                                                                           >  1:387685/1‑149 (MQ=255)
                                                   tggAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAg                                                                                         <  2:436217/148‑1 (MQ=255)
                                                        agagaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGc                                                                                    >  1:33461/1‑149 (MQ=255)
                                                        acagaAATATTGCGCTTCATGGGCCGGGGCTACTCAATGACACAAATTGCCGAGTAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGc                                                                                    <  1:196783/147‑1 (MQ=255)
                                                          agaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCTGGGTTGTTGGAGGCCGccg                                                                                  >  2:476696/1‑147 (MQ=255)
                                                                  ggtgcggtATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTg                                                                          <  2:361898/142‑1 (MQ=255)
                                                                      cTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTAGGGGTCAGTTCTTCAGCAGGGTTGTTGGAGGCCACAGATACTCTGTtat                                                                      >  2:142738/1‑149 (MQ=255)
                                                                         tATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtatgta                                                                   <  2:595158/149‑1 (MQ=255)
                                                                            gTCGCGTGGCTACTAAATGAGACAAAGTGCCGAGCAGGTTAAACGCACTATCATACCGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCTGATATTCTGTTATGTATGc                                                                <  2:531837/149‑1 (MQ=255)
                                                                                  tGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCAtt                                                          >  1:415842/1‑149 (MQ=255)
                                                                                     cTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGAACTTCTGTTATGTATGCGGCATTGCg                                                       >  1:72720/1‑149 (MQ=255)
                                                                                        cgcAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaac                                                    <  2:374747/147‑2 (MQ=255)
                                                                                        cTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaaa                                                    >  1:278933/1‑149 (MQ=255)
                                                                                           aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATATGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                                 >  1:639526/1‑149 (MQ=255)
                                                                                            aTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAg                                                >  1:221484/1‑149 (MQ=255)
                                                                                            aTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGCGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAg                                                >  1:639692/1‑149 (MQ=255)
                                                                                            aTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGAGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAg                                                >  1:640016/1‑149 (MQ=255)
                                                                                            aTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAAGTTAATGTGATGTGGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAg                                                <  1:366365/149‑1 (MQ=255)
                                                                                               acacAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCGGCAGATATTCTGTGATGTATGCGGCATTGCGAAACAAGTaa                                             >  1:502266/1‑149 (MQ=255)
                                                                                                    aaTTGCCCACCAGCTTAAACGCAATATCAAAACGATCCTTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGTGTTGTTGGATGCCGCAGATATTCTGTTATGTATTCGGCATTGCGAAACAAGTAATgtgt                                        <  1:183445/149‑1 (MQ=255)
                                                                                                            actagcTTAAACTCAATAGCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATccc                                <  1:206477/146‑1 (MQ=255)
                                                                                                              caagttAAAGCCAAGATAAAAACGCTCCGTTAACATAAATTTCATGTTATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTGTGACGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTa                              <  2:232519/145‑1 (MQ=255)
                                                                                                                gcTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTAtt                            >  1:75878/1‑149 (MQ=255)
                                                                                                                gcTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTAAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCGTAtt                            >  1:305532/1‑149 (MQ=255)
                                                                                                                    aaaCGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGACGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATc                        <  1:425313/149‑1 (MQ=255)
                                                                                                                     aaCGCAATATCAAAACGAACCGTGAAACTAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATcc                       <  1:99870/149‑1 (MQ=255)
                                                                                                                      aCGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCg                      >  1:515557/1‑149 (MQ=255)
                                                                                                                                aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCg            <  1:369381/149‑1 (MQ=255)
                                                                                                                                  aaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCggg          <  1:120912/149‑1 (MQ=255)
                                                                                                                                       tCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTCCTGACGCAGGGTTCTTGGAGGCCGCAGACATTCTGTTATGTATGCGGCCTTGCGACACAAGTACTGTGTTGCATCCCTCTCAATGCGCATGATGCCGGGTCTAc     >  2:379970/1‑149 (MQ=255)
                                                                                                                                        ccGTGAACATAAATTTAATGGGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGAGATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGGTTACt    <  2:314670/149‑1 (MQ=255)
                                                                                                                                          gTGAACATAAATTTAATGTGATGTCAAAACAGGGCGTGAGTTCTGACACAGGGTTGTTGGAGGCCGCAGAGATTCTGTTATGTATGCGGCATTACGAAACAAGTAAAGTGTAGCATCCGTGTTAATCAGCTTGATGCGGGACTTACTTc  >  2:538195/1‑149 (MQ=255)
                                                                                                                                             |                                                                                                                                                 
ACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_pae_tpiA/4604491‑4604777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A