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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 454,989 C→G 16.2% L32L (CTG→CTC)  ybgH ← predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE454,9890CG16.2% 157.6 / 22.6 68L32L (CTG→CTC) ybgHpredicted transporter
Reads supporting (aligned to +/- strand):  ref base C (26/31);  new base G (3/8);  total (29/39)
Fisher's exact test for biased strand distribution p-value = 3.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATA  >  minE/454921‑455055
                                                                    |                                                                  
cAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATcag                                                                  <  1:3708586/71‑1 (MQ=255)
cAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATcag                                                                  <  1:3586837/71‑1 (MQ=255)
  gTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATcagc                                                                 <  1:1765773/70‑1 (MQ=255)
  gTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATcag                                                                  >  1:3571204/1‑69 (MQ=255)
        gcTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCAc                                                          <  1:2538141/71‑1 (MQ=255)
         cTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACg                                                         <  1:2607543/71‑1 (MQ=255)
            aaTAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCAt                                                      <  1:139096/71‑1 (MQ=255)
             aTAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCAt                                                      <  1:1014072/70‑1 (MQ=255)
             aTAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATg                                                     <  1:2499243/71‑1 (MQ=255)
              tAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGc                                                    <  1:754617/71‑1 (MQ=255)
              tAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGc                                                    >  1:2646086/1‑71 (MQ=255)
                aCTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCg                                                  <  1:2713603/71‑1 (MQ=255)
                 cTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCg                                                  >  1:3646856/1‑70 (MQ=255)
                    gTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa                                               >  1:459620/1‑70 (MQ=255)
                    gTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa                                               >  1:2412742/1‑70 (MQ=255)
                    gTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa                                               >  1:2358149/1‑70 (MQ=255)
                    gTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa                                               >  1:444932/1‑70 (MQ=255)
                    gTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa                                               <  1:1299840/70‑1 (MQ=255)
                    gTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa                                               <  1:2143446/70‑1 (MQ=255)
                    gTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa                                               >  1:594306/1‑70 (MQ=255)
                    gTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTaa                                               >  1:598975/1‑70 (MQ=255)
                          gTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTaa                                        <  1:3734603/71‑1 (MQ=255)
                          gTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTa                                         >  1:521910/1‑70 (MQ=255)
                           tGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTaa                                        >  1:872901/1‑70 (MQ=255)
                             aGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAat                                     <  1:1637887/71‑1 (MQ=255)
                              gTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGt                                                 <  1:3472690/58‑1 (MQ=255)
                              gTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAata                                    <  1:3885647/71‑1 (MQ=255)
                              gTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAata                                    >  1:1974156/1‑71 (MQ=255)
                               tATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGt                                                 >  1:3491445/1‑57 (MQ=255)
                               tATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAatat                                   <  1:1047257/71‑1 (MQ=255)
                               tATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAatat                                   >  1:808394/1‑71 (MQ=255)
                               tATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAatat                                   <  1:2942021/71‑1 (MQ=255)
                                 tCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCAt                                                      >  1:3520769/1‑50 (MQ=255)
                                  cGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTc                                 >  1:3907370/1‑70 (MQ=255)
                                  cGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTc                                 >  1:3902917/1‑70 (MQ=255)
                                         ttttAGTTGATTGGTGAGATAGAGAATCAGCAggg                                                             <  1:2219114/35‑1 (MQ=255)
                                         ttttAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGAttt                         <  1:3918520/71‑1 (MQ=255)
                                         ttttAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGAttt                         >  1:3281715/1‑71 (MQ=255)
                                           ttAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTg                        <  1:3659346/70‑1 (MQ=255)
                                           ttAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTg                        <  1:1724126/70‑1 (MQ=255)
                                           ttAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTg                        <  1:1455450/70‑1 (MQ=255)
                                            tAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCa                                                       >  1:2754271/1‑38 (MQ=255)
                                              gTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTaaaa                                      >  1:1556433/1‑53 (MQ=255)
                                                  atgggTGAGATAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGAtcgc                  <  1:2110966/66‑1 (MQ=255)
                                                  atgggTGAGATAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGAtcgc                  <  1:594407/66‑1 (MQ=255)
                                                   ttGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCaa                >  1:3571166/1‑70 (MQ=255)
                                                    tGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCaa                >  1:2071687/1‑69 (MQ=255)
                                                    gggTGAGATAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTg                        >  1:3637716/2‑61 (MQ=255)
                                                     ggTGAGATAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACg              <  1:3413146/70‑1 (MQ=255)
                                                     ggTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACg              <  1:1588269/70‑1 (MQ=255)
                                                       tGAGATAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGata           <  1:479848/71‑3 (MQ=255)
                                                        gagaTAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACa           >  1:2183757/1‑70 (MQ=255)
                                                         agaTAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGAtata         <  1:1031011/71‑1 (MQ=255)
                                                           aTAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGc                       >  1:2157446/1‑55 (MQ=255)
                                                           aTAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGt       <  1:2289002/71‑1 (MQ=255)
                                                            tAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTa      >  1:1461850/1‑71 (MQ=255)
                                                            tAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAata                                    <  1:43173/41‑1 (MQ=255)
                                                            tAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAata                                    <  1:2343091/41‑1 (MQ=255)
                                                            tAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAata                                    <  1:47862/41‑1 (MQ=255)
                                                            tAGAGAATCAGCAGGACACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTa      <  1:220749/71‑1 (MQ=255)
                                                             agagAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAgcgc                  <  1:2383786/58‑1 (MQ=255)
                                                              gagaATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTata    <  1:2013045/71‑3 (MQ=255)
                                                              gagaATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTaaa    <  1:1366534/71‑1 (MQ=255)
                                                              gagaATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTaaa    <  1:3595261/71‑1 (MQ=255)
                                                              gagaATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTaaa    <  1:1765787/71‑1 (MQ=255)
                                                               agaATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGAtata         <  1:3048127/65‑1 (MQ=255)
                                                               agaATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATAtt                                  >  1:3915264/1‑40 (MQ=255)
                                                               agaATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATAtt                                  >  1:1788054/1‑40 (MQ=255)
                                                               agaATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATAtt                                  >  1:2882151/1‑40 (MQ=255)
                                                                gaATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTatatc  >  1:665482/1‑70 (MQ=255)
                                                                gaATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTatatc  <  1:3408650/71‑2 (MQ=255)
                                                                gaATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAAt   <  1:1390922/70‑1 (MQ=255)
                                                                    |                                                                  
CAGTAGGCGCTAAATAACTCGTAGGCGTGAGTATCGTTGTATTTTAGTTGATTGGTGAGATAGAGAATCAGCAGGGCACGCATGCCGTAAAAGCTAAAATATTCCCAGATTTGCAGCGCAACGACATAGTAAATA  >  minE/454921‑455055

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