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 1,211,319 G→A 18.2% F11F (TTC→TTT)  cspC ← stress protein, member of the CspA‑family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,211,3190GA18.2% 202.8 / 34.2 88F11F (TTC→TTT) cspCstress protein, member of the CspA‑family
Reads supporting (aligned to +/- strand):  ref base G (31/41);  new base A (10/6);  total (41/47)
Fisher's exact test for biased strand distribution p-value = 1.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.81e-01

CGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCGCAGG  >  minE/1211249‑1211388
                                                                      |                                                                     
cGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTg                                                                       <  1:2159560/71‑1 (MQ=255)
   agaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAc                                                                    >  1:2135013/1‑71 (MQ=255)
   agaAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAAc                                                                    >  1:3516745/1‑71 (MQ=255)
   agaAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAAc                                                                    >  1:3304559/1‑71 (MQ=255)
   agaAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAAc                                                                    >  1:1887077/1‑71 (MQ=255)
    gaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAcc                                                                   <  1:699068/71‑1 (MQ=255)
      aGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCAc                                                                 <  1:1681386/71‑1 (MQ=255)
        tgtACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACtt                                                               <  1:3909223/71‑1 (MQ=12)
         gtACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCTAAACCTTTAGACTCGTTGAACCACtt                                                               >  1:868425/1‑70 (MQ=255)
         gtACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACtt                                                               >  1:845793/1‑70 (MQ=255)
          tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTaaa                                                                     >  1:578390/1‑63 (MQ=9)
          tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTa                                                              <  1:1194781/70‑1 (MQ=255)
           aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAAc                                                            >  1:530704/1‑71 (MQ=255)
            cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcg                                                           >  1:1793018/1‑70 (MQ=255)
                cacaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGAc                                                       <  1:2904577/71‑1 (MQ=255)
                cacaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGAc                                                       >  1:3287333/1‑71 (MQ=255)
                 acaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCt                                                          <  1:2200473/67‑1 (MQ=255)
                 aaaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGAc                                                       >  1:263882/3‑70 (MQ=255)
                   gtCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCtt                                                    >  1:1462865/2‑71 (MQ=255)
                   aTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCtt                                                    <  1:1820088/71‑1 (MQ=255)
                     cTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCtt                                                    >  1:2838813/1‑69 (MQ=255)
                     cTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGaa                                                                     >  1:1231530/1‑52 (MQ=255)
                     cTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCttt                                                   >  1:3855000/1‑70 (MQ=255)
                        tgctgcCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTa                                                              >  1:3592555/1‑56 (MQ=255)
                        tgctgcCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTa                                                              >  1:111644/1‑56 (MQ=255)
                        tgctgcCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATc                                               >  1:2031568/1‑71 (MQ=255)
                        tgctgcCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATc                                               >  1:1210538/1‑71 (MQ=255)
                        tgctgcCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATc                                               >  1:2793454/1‑71 (MQ=255)
                          ctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCtt                                             <  1:501487/71‑1 (MQ=255)
                          ctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCtt                                             <  1:1277899/71‑1 (MQ=255)
                          ctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCtt                                             <  1:83884/71‑1 (MQ=255)
                           tgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTg                                                                       <  1:1698098/44‑1 (MQ=255)
                              cATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGcc                                         <  1:3587172/71‑1 (MQ=255)
                               aTCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                                                        >  1:2382057/1‑55 (MQ=255)
                               aTCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCa                                        <  1:3058124/71‑1 (MQ=255)
                                tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAAcc                                                                   <  1:998981/43‑1 (MQ=255)
                                tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAAcc                                                                   <  1:690369/43‑1 (MQ=255)
                                tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                                       <  1:1016430/71‑1 (MQ=255)
                                tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                                       <  1:2182732/71‑1 (MQ=255)
                                  ttccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtc                                      >  1:2289156/3‑69 (MQ=255)
                                  aGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAttt                                     >  1:2278971/1‑71 (MQ=255)
                                  aGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAttt                                     <  1:3669882/71‑1 (MQ=255)
                                  aGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAtt                                      <  1:992184/70‑1 (MQ=255)
                                   tccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCtt                                                    <  1:2279505/54‑1 (MQ=16)
                                   gCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTg                                    <  1:3357793/71‑1 (MQ=255)
                                    ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTaa                                                 <  1:131685/57‑1 (MQ=255)
                                    ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTaa                                                 <  1:1532320/57‑1 (MQ=255)
                                       gAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                                       <  1:1934341/64‑1 (MQ=255)
                                        aGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGAc                                                       <  1:2600584/47‑1 (MQ=255)
                                        aGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa                               <  1:1373721/71‑1 (MQ=255)
                                         gTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGATAAAt                              >  1:2332611/1‑71 (MQ=255)
                                          tAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTg                                                         <  1:174917/43‑1 (MQ=255)
                                          tAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAAtt                             <  1:354049/71‑1 (MQ=255)
                                          tAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAAt                              <  1:1242601/70‑1 (MQ=255)
                                            aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAttt                                     >  1:3767160/1‑61 (MQ=255)
                                            aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc                           >  1:901757/1‑71 (MQ=255)
                                                aGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAg                       <  1:1061082/71‑1 (MQ=255)
                                                 gCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGa                      <  1:1836371/71‑1 (MQ=255)
                                                   cAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGact                    >  1:1847833/1‑69 (MQ=255)
                                                   cAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGAt                     >  1:446508/1‑70 (MQ=255)
                                                    aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAttt                                     >  1:3183931/1‑53 (MQ=255)
                                                    aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTg                   <  1:1081798/71‑1 (MQ=255)
                                                    aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTg                   >  1:3707406/1‑71 (MQ=255)
                                                     aaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCt                          <  1:1876481/63‑1 (MQ=255)
                                                       aCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGttt                >  1:582833/1‑71 (MQ=255)
                                                        ccTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCttt                                            >  1:3533376/1‑42 (MQ=255)
                                                        ccTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGtttt               <  1:3845560/71‑1 (MQ=255)
                                                        ccTTTAGAATCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGtttt               <  1:42467/71‑1 (MQ=255)
                                                         cTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGtttt               <  1:2472973/70‑1 (MQ=255)
                                                           ttAGACTCGTTGAAGCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTttct             >  1:3740998/1‑70 (MQ=255)
                                                           ttAGACTCGTTGAACCACTTAACCTGACCTTTAATCt                                              <  1:2574013/37‑1 (MQ=255)
                                                           ttAGACTCGTTGAACCACTTAACCTGACCTTTAATCt                                              <  1:1715342/37‑1 (MQ=255)
                                                           ttAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTttct             >  1:3428869/1‑70 (MQ=255)
                                                             aGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTttcttc           <  1:724211/70‑1 (MQ=255)
                                                              gACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCg          <  1:1204728/70‑1 (MQ=255)
                                                                cTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTc                            <  1:3792746/50‑1 (MQ=255)
                                                                 tCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa                               >  1:1745581/1‑46 (MQ=255)
                                                                 tCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaa                                 <  1:363604/44‑1 (MQ=255)
                                                                 tCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGa                                   >  1:3587630/1‑42 (MQ=255)
                                                                 tCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc                           <  1:667791/50‑1 (MQ=255)
                                                                 tCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCg      >  1:441598/1‑71 (MQ=255)
                                                                 tCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCg      >  1:3434377/1‑71 (MQ=255)
                                                                  cGTTGAACCACTTAACCTGACCTTTAATCTTTGcc                                         <  1:3821576/35‑1 (MQ=255)
                                                                  cGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCg      >  1:1961516/1‑70 (MQ=255)
                                                                   gTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCg      <  1:3833906/69‑1 (MQ=255)
                                                                   gTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCg      <  1:2703936/69‑1 (MQ=255)
                                                                   gTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCg      <  1:3703480/69‑1 (MQ=255)
                                                                   gTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCGc     <  1:2039115/70‑1 (MQ=255)
                                                                   gTTGAACCACTTAACCTGACCGTTAATCTTTGCCATTTGAAAAATTCCtt                         >  1:754489/1‑50 (MQ=255)
                                                                     tGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCtt                         >  1:2735142/1‑48 (MQ=255)
                                                                     tGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCAGCAgg  >  1:1399468/1‑71 (MQ=255)
                                                                      |                                                                     
CGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCGCAGG  >  minE/1211249‑1211388

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