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 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 835,178 T→C 9.6% Y1212Y (TAT→TAC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,1780TC 9.6% 209.8 / 11.4 73Y1212Y (TAT→TAC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (37/29);  new base C (5/2);  total (42/31)
Fisher's exact test for biased strand distribution p-value = 6.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAT  >  minE/835108‑835247
                                                                      |                                                                     
cccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTAt                                                                       <  1:2930574/71‑1 (MQ=255)
   gTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGc                                                                    <  1:26367/71‑1 (MQ=255)
        aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                                               <  1:3088007/71‑1 (MQ=255)
         cGCCGAAACGCACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTa                                                              <  1:3688406/71‑1 (MQ=255)
         cGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTa                                                              <  1:2263758/71‑1 (MQ=255)
          gCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAg                                                             <  1:3084032/71‑1 (MQ=255)
           ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAgg                                                            >  1:3466709/1‑71 (MQ=255)
           ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAgg                                                            >  1:530452/1‑71 (MQ=255)
            cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                                                      >  1:3650211/1‑60 (MQ=255)
            cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                                                      >  1:2442846/1‑60 (MQ=255)
            cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                                                      >  1:909239/1‑60 (MQ=255)
            cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                                                      >  1:2168642/1‑60 (MQ=255)
            cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                           <  1:109088/71‑1 (MQ=255)
            cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                                                           <  1:1185876/71‑1 (MQ=255)
             gAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCgg                                                            >  1:408821/1‑69 (MQ=255)
              aaaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGGACCGTCggat                                                          >  1:1525433/1‑68 (MQ=255)
              aaaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                                               >  1:24556/1‑65 (MQ=255)
              aaaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATc                                                         >  1:1549236/1‑71 (MQ=255)
               aaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATc                                                         >  1:2450242/1‑70 (MQ=255)
                aCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                                        >  1:2220365/1‑70 (MQ=255)
                aCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATcga                                                       <  1:816707/71‑3 (MQ=255)
                 ccGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                                                      <  1:355606/71‑1 (MQ=255)
                    aCGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcg                                                   >  1:2983578/1‑71 (MQ=255)
                    aCGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcg                                                   >  1:604286/1‑71 (MQ=255)
                     cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                                                  <  1:1218457/71‑1 (MQ=255)
                      gCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgcg                                                 <  1:2561273/71‑1 (MQ=255)
                        atatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt                                               <  1:200674/71‑1 (MQ=255)
                        atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                               >  1:3215670/1‑71 (MQ=255)
                        atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                               >  1:98069/1‑71 (MQ=255)
                          atGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                                               >  1:3049761/1‑69 (MQ=255)
                             aTCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGtt                                          <  1:2785975/71‑1 (MQ=255)
                                ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgt                                       >  1:1556131/1‑71 (MQ=255)
                                ggcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgt                                       <  1:3327877/71‑1 (MQ=255)
                                  cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                     <  1:3675487/71‑1 (MQ=255)
                                   ggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                    <  1:2664677/71‑1 (MQ=255)
                                   ggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                    <  1:3690880/71‑1 (MQ=255)
                                   ggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                    <  1:1734870/71‑1 (MQ=255)
                                    gcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                     >  1:2686193/1‑69 (MQ=255)
                                    gcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                     >  1:2177215/1‑69 (MQ=255)
                                       aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTg                                >  1:727580/1‑71 (MQ=255)
                                        tGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                                              >  1:1602763/1‑56 (MQ=255)
                                        tGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                     <  1:3122389/65‑1 (MQ=255)
                                            cATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                             >  1:2342998/1‑69 (MQ=255)
                                             aTCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                             >  1:3067849/1‑68 (MQ=255)
                                                tGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                                                          >  1:131592/1‑36 (MQ=255)
                                                tGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAg                          >  1:804932/1‑68 (MQ=255)
                                                  gCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCTATGAGTTTGTTGTAGTGCGTAAGATga                      <  1:3546/70‑1 (MQ=255)
                                                  gCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCTATGAGTTTGTTGTAGTGCGTAAGATga                      <  1:1801173/70‑1 (MQ=255)
                                                  gCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATg                       <  1:1718797/69‑1 (MQ=255)
                                                     tACGGCTTTAACTACTATGGCACCGTAGGTTCTAAcc                                                    <  1:1314845/37‑1 (MQ=255)
                                                     tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                  >  1:2276106/1‑71 (MQ=255)
                                                     tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                  >  1:3550476/1‑71 (MQ=255)
                                                     tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag                    <  1:1816253/69‑1 (MQ=255)
                                                       cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt                                 >  1:114608/1‑54 (MQ=255)
                                                       cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAAc                 <  1:2503628/70‑1 (MQ=255)
                                                       cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                <  1:878151/71‑1 (MQ=255)
                                                       cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                <  1:266581/71‑1 (MQ=255)
                                                        ggCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAt               >  1:3114466/1‑71 (MQ=255)
                                                           tttAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATga                      <  1:2844417/61‑1 (MQ=255)
                                                           tttAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATga                      <  1:3452892/61‑1 (MQ=255)
                                                             tAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGtt                                          >  1:2389628/1‑39 (MQ=255)
                                                             tAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt          >  1:99290/1‑71 (MQ=255)
                                                             tAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt          >  1:1697763/1‑71 (MQ=255)
                                                             tAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt          >  1:3390692/1‑71 (MQ=255)
                                                             tAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt          >  1:454501/1‑71 (MQ=255)
                                                               actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTg         <  1:3275510/70‑1 (MQ=255)
                                                                ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt       >  1:423842/1‑71 (MQ=255)
                                                                   ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGAt                        <  1:603014/51‑1 (MQ=255)
                                                                   ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt              >  1:2625679/1‑61 (MQ=255)
                                                                     aTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                     >  1:2611098/1‑52 (MQ=255)
                                                                     aTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                     >  1:529662/1‑52 (MQ=255)
                                                                     aTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                     >  1:3218340/1‑52 (MQ=255)
                                                                     aTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                     >  1:3437243/1‑52 (MQ=255)
                                                                     aTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt  >  1:88283/1‑71 (MQ=255)
                                                                      tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGtt      >  1:287978/1‑66 (MQ=255)
                                                                      tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt  <  1:569843/70‑1 (MQ=255)
                                                                      tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt  <  1:2075129/70‑1 (MQ=255)
                                                                      tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt  <  1:827336/70‑1 (MQ=255)
                                                                      tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt  <  1:1213042/70‑1 (MQ=255)
                                                                      tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt  <  1:3485146/70‑1 (MQ=255)
                                                                      |                                                                     
CCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAT  >  minE/835108‑835247

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