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 F61 I0 R1 274 47.1 1889746 95.1% 1797148 135.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 4,178,209 C→T 14.0% R978C (CGT→TGT)  rpoC → RNA polymerase, beta prime subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092734,178,2090CT14.0% 137.1 / 14.0 50R978C (CGT→TGT) rpoCRNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand):  ref base C (15/28);  new base T (2/5);  total (17/33)
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

CATCGGTGGTGCGGCATCTCGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAACTGGGACCCGCAC  >  CP009273/4178085‑4178346
                                                                                                                            |                                                                                                                                         
caTCGGTGGTGCGGCATCTCGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATactgaactga                                                                                                                            >  2:670922/1‑140 (MQ=255)
        gtgCGGCATCTCGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATc                                                                                                                    >  1:86747/1‑140 (MQ=255)
        gtgCGGCATCTCGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATc                                                                                                                    >  1:347493/1‑140 (MQ=255)
                  tcGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCg                                                                                                          >  1:812720/1‑140 (MQ=255)
                   cGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCgg                                                                                                         >  1:727932/1‑140 (MQ=255)
                   cGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCgg                                                                                                         <  1:666783/140‑1 (MQ=255)
                   cGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCgg                                                                                                         <  1:632497/140‑1 (MQ=255)
                       cGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGt                                                                                                     <  2:86747/140‑1 (MQ=255)
                        ggCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTa                                                                                                    >  2:861682/1‑140 (MQ=255)
                        ggCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTa                                                                                                    >  2:720204/1‑140 (MQ=255)
                        ggCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGGGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTa                                                                                                    >  2:48668/1‑140 (MQ=255)
                        ggCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGCAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTa                                                                                                    >  1:383033/1‑140 (MQ=255)
                                aaTCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTaaagaa                                                                                            <  1:578628/140‑1 (MQ=255)
                                aaTCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTaaagaa                                                                                            <  1:459269/140‑1 (MQ=255)
                                aaTCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTaaagaa                                                                                            <  1:941474/140‑1 (MQ=255)
                                       cATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACa                                                                                     <  2:632283/140‑1 (MQ=255)
                                       cATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACa                                                                                     <  2:564102/140‑1 (MQ=255)
                                       cATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACa                                                                                     <  2:581350/140‑1 (MQ=255)
                                           cAAGTGAAAAACAAAGGTAGCATGAAGCTCAGCAACGTGAAGTCGTTTGTGAACTCCAGCGGTAATCTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGt                                                                                 <  2:861902/140‑1 (MQ=255)
                                                 aaaaaCAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCTGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTa                                                                           <  2:324037/140‑1 (MQ=255)
                                                 aaaaaCAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCTGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTa                                                                           <  2:288287/140‑1 (MQ=255)
                                                 aaaaaCAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCTGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTa                                                                           <  1:317138/140‑1 (MQ=255)
                                                 aaaaaCAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCTGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTa                                                                           <  1:316925/140‑1 (MQ=255)
                                                  acaaCAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTAc                                                                          <  1:35488/138‑1 (MQ=255)
                                                      cAAAGGTAGCATCAAGCTCATCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTg                                                                      <  2:264282/140‑1 (MQ=255)
                                                      cAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTg                                                                      <  2:264248/140‑1 (MQ=255)
                                                      cAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTg                                                                      <  2:35491/140‑1 (MQ=255)
                                                      cAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTg                                                                      <  1:883658/140‑1 (MQ=255)
                                                      cAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTg                                                                      <  1:326852/140‑1 (MQ=255)
                                                      cAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTg                                                                      <  1:586101/140‑1 (MQ=255)
                                                      cAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCGTACGGTg                                                                      <  1:324750/140‑1 (MQ=255)
                                                      cAAAGGTAGCATCAAGCACAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTg                                                                      <  1:737689/140‑1 (MQ=255)
                                                                        cAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCg                                                    <  2:812720/140‑1 (MQ=255)
                                                                         aGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGa                                                   <  1:99402/140‑1 (MQ=255)
                                                                          gCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGAt                                                  >  1:730165/1‑140 (MQ=255)
                                                                          gCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGAt                                                  >  1:582232/1‑140 (MQ=255)
                                                                                tGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGaa                                            <  2:582232/140‑1 (MQ=255)
                                                                                tGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGaa                                            <  2:730165/140‑1 (MQ=255)
                                                                                tGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACGACAGAAAGCTACAAAGTACCTGACGGTGCGGTACTGGCGAAAGGCGATGGCGaa                                            <  1:591844/140‑1 (MQ=255)
                                                                                   aGTCGGTTGTGAACTCCAGCGGTCAACTGGTTATCACTTCCTGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAg                                         >  1:221804/1‑140 (MQ=255)
                                                                                   aGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCTGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGACCAg                                         >  1:652322/1‑140 (MQ=255)
                                                                                     tCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGt                                       >  1:79996/1‑140 (MQ=255)
                                                                                     tCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGt                                       >  1:785289/1‑140 (MQ=255)
                                                                                     tCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGt                                       >  1:58033/1‑140 (MQ=255)
                                                                                                 tCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGa                           <  2:158310/140‑1 (MQ=255)
                                                                                                          aaaCTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAACGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGc                  <  1:632474/140‑1 (MQ=255)
                                                                                                          aaaCTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGc                  <  2:383033/140‑1 (MQ=255)
                                                                                                                gTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAACTg            >  1:278666/1‑140 (MQ=255)
                                                                                                                         tCCTGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAACTGGGACCCGca   <  1:821709/140‑1 (MQ=255)
                                                                                                                         tCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAACTGGGACCCGca   <  1:670922/140‑1 (MQ=255)
                                                                                                                          cccGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAACTGGGACCCGcac  >  1:532178/1‑140 (MQ=255)
                                                                                                                          cccGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAACTGGGACCCGcac  >  1:194732/1‑140 (MQ=255)
                                                                                                                          cccGTAATACTGAACTGAAACTGATCGACCAATTCGGTCGTACTAAAGAAAGCTACACAGTACCTTACGGTGAGGTAATGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAACTGGGACCCGcac  >  1:394895/1‑140 (MQ=255)
                                                                                                                            |                                                                                                                                         
CATCGGTGGTGCGGCATCTCGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAACTGGGACCCGCAC  >  CP009273/4178085‑4178346

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A