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 834,842 C→A 14.4% S1100S (TCC→TCA)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE834,8420CA14.4% 205.5 / 14.1 69S1100S (TCC→TCA) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (32/27);  new base A (5/5);  total (37/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.24e-01

AATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTGAAGCC  >  minE/834775‑834911
                                                                   |                                                                     
aaTCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCAcc                                                                    <  1:2703181/71‑1 (MQ=255)
  tCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTa                                                                  <  1:3760787/71‑1 (MQ=255)
     aaCGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAg                                                               <  1:1480153/71‑1 (MQ=255)
      aCGGCTTCCCGGAAAAAGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAgt                                                              <  1:3301603/71‑2 (MQ=255)
       cGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtccactcca                                                                      >  1:1097051/1‑62 (MQ=255)
       cGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGc                                                              >  1:1278335/1‑70 (MQ=255)
             cccggAAAAAGCACTTAACTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGaaaa                                                         <  1:502034/66‑1 (MQ=255)
             ccAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTa                                                                  >  1:2827921/1‑60 (MQ=255)
             ccAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAAcc                                                       >  1:2987851/1‑71 (MQ=255)
              cAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCt                                                                   <  1:3233642/58‑1 (MQ=255)
               aGGATAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCg                                                             <  1:3719383/63‑1 (MQ=255)
               aGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACctg                                                     <  1:1647254/71‑1 (MQ=255)
                ggAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACctgc                                                    >  1:3222517/1‑71 (MQ=255)
                ggAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACctg                                                     >  1:1773966/1‑70 (MQ=255)
                 gAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTAc                                                                 <  1:635203/57‑1 (MQ=255)
                 gAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACctgct                                                   <  1:3359566/71‑1 (MQ=255)
                  aaaaaGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtccactccac                                                                     >  1:493546/1‑52 (MQ=255)
                  aaaaaGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACctgct                                                   >  1:1239461/1‑70 (MQ=255)
                   aaaaGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctga                                                 >  1:3368332/1‑71 (MQ=255)
                      aGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctgatgc                                              >  1:471461/1‑71 (MQ=255)
                          cttaaCTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCTGCTAATGCTGAc                                          >  1:92381/4‑71 (MQ=255)
                          cTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACct                                                      >  1:2632749/1‑59 (MQ=255)
                           ttaaCTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCtgctaatgctga                                           <  1:3420312/67‑1 (MQ=255)
                           tCAACTTCCTGACGCCGCACCAGAAGTGGGGTAtccactcca                                                                      >  1:2996528/1‑42 (MQ=255)
                           tCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGAc                                                           >  1:3270975/1‑53 (MQ=255)
                           tCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGAc                                                           >  1:3593428/1‑53 (MQ=255)
                           tCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGAc                                                           >  1:1547893/1‑53 (MQ=255)
                            taaCTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTa                                                                  >  1:2186925/2‑45 (MQ=25)
                            taaCTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTa                                                                  >  1:2115153/2‑45 (MQ=25)
                             accTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACtt                                        <  1:1784542/68‑1 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCttctgatgct                                             >  1:1950809/1‑65 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctgatgct                                             <  1:3065896/65‑1 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctgatgct                                             >  1:1164855/1‑65 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctga                                                 <  1:3378406/61‑1 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctga                                                 <  1:3414901/61‑1 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctga                                                 <  1:3809407/61‑1 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACttt                                       <  1:1815356/71‑1 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACttt                                       <  1:2880739/71‑1 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACtt                                        <  1:2077079/70‑1 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACtt                                        >  1:2004276/1‑70 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCTGCTAATGCTGAcgct                                       >  1:1137890/1‑68 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCTGCTAATGCTGAcgct                                       >  1:3011110/1‑68 (MQ=255)
                             aaCTTCCTGACGCCGCACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCTGCTAATGCTGAcg                                         <  1:3897939/69‑2 (MQ=255)
                              aCTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACttt                                       <  1:3239949/70‑1 (MQ=255)
                                ttCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAgg                                    >  1:523305/1‑71 (MQ=255)
                                 tCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCtgctgatg                                               >  1:3638768/1‑59 (MQ=255)
                                 tCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGAc                                          >  1:2403516/1‑64 (MQ=255)
                                  ccTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGt                                   <  1:2850014/70‑1 (MQ=255)
                                   cTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTcg                                 <  1:910813/71‑1 (MQ=255)
                                      aCGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGc                                                              >  1:3915758/1‑39 (MQ=255)
                                      aCGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGgcgctg                              <  1:440874/71‑3 (MQ=255)
                                      aCGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGcgg                              <  1:3023732/71‑1 (MQ=255)
                                      aCGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGcgg                              <  1:2389547/71‑1 (MQ=255)
                                      aCGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGcgg                              <  1:404062/71‑1 (MQ=255)
                                         ccgcACCAGAAATGGGGCATTCACTCAACCTACAGTGAAAACCTGCTAATGCTGACGCTCTCTCGcggtgg                           <  1:1357948/71‑1 (MQ=255)
                                           gcACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTa                                      >  1:3388997/1‑58 (MQ=255)
                                           gcACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTa                                      >  1:3895735/1‑58 (MQ=255)
                                           gcACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGcggtggt                          >  1:1028919/1‑70 (MQ=255)
                                             aCCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAgg                                    >  1:3205978/1‑58 (MQ=255)
                                             aCCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAgg                                    >  1:3117071/1‑58 (MQ=255)
                                              ccAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGcggtggtccgg                      <  1:1066846/71‑1 (MQ=255)
                                                aGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGcggtggtccggtg                    >  1:1695133/1‑71 (MQ=255)
                                                 gAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTcgcg                               >  1:1823140/1‑59 (MQ=255)
                                                 gAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGcggtggtccggtgg                   >  1:850214/1‑71 (MQ=255)
                                                 gAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGcggtggtccggtgg                   >  1:256754/1‑71 (MQ=255)
                                                    gTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCt                >  1:1006801/1‑71 (MQ=255)
                                                      ggggTATCCACTCCACCTACAGCGACAACCTGCTTATGCTGACTTTAGGTCGcggt                             <  1:2391963/56‑1 (MQ=255)
                                                       gggTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGt             >  1:290169/1‑71 (MQ=255)
                                                        ggTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGtt            <  1:374674/71‑1 (MQ=255)
                                                        ggTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGGCGCGGTGGTCCGGTGGTCTGGtt            <  1:2154210/71‑1 (MQ=255)
                                                           aTCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAg         >  1:1400834/1‑71 (MQ=255)
                                                           aTCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAg         >  1:1911405/1‑71 (MQ=255)
                                                            tccactccacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAg         >  1:3227962/1‑70 (MQ=255)
                                                            tccactccacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGt        >  1:815610/1‑71 (MQ=255)
                                                              cactccacCTACAGCGACAACCTGCTGATGCTGACtt                                        <  1:2898683/37‑1 (MQ=255)
                                                              cactccacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTg       >  1:1199259/1‑70 (MQ=255)
                                                              cactccacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTGa      <  1:134539/71‑1 (MQ=255)
                                                              cactccacCTACAGCGACAACCTGCTGATGATGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTg       <  1:2986588/70‑1 (MQ=255)
                                                               actccacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTg       >  1:1251685/1‑69 (MQ=255)
                                                               actacacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGa          >  1:3088452/1‑66 (MQ=255)
                                                                ctccacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTGAAg    >  1:389281/1‑71 (MQ=255)
                                                                  ccacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTGAAGcc  >  1:2838486/1‑71 (MQ=255)
                                                                   cacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTGAAGcc  >  1:2405061/1‑70 (MQ=255)
                                                                   cacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTGAAGcc  <  1:1595924/70‑1 (MQ=255)
                                                                   cacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTGAAGcc  >  1:2409675/1‑70 (MQ=255)
                                                                   cacCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTGAAGc   >  1:822365/1‑69 (MQ=255)
                                                                   |                                                                     
AATCCAACGGCAACCAGGAAAAAGCGCTCAACTTCCTGACGCCGCACCAGAAGTGGGGTATCCACTCCACCTACAGCGACAACCTGCTGATGCTGACTTTAGGTCGCGGTGGTCCGGTGGTCTGGTTGAGTGAAGCC  >  minE/834775‑834911

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