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 832,268 T→C 27.3% A242A (GCT→GCC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,2680TC27.3% 118.2 / 51.6 77A242A (GCT→GCC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (21/35);  new base C (9/12);  total (30/47)
Fisher's exact test for biased strand distribution p-value = 7.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

CTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATG  >  minE/832199‑832335
                                                                     |                                                                   
cTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATctgctg                                                                    <  1:2482226/71‑1 (MQ=255)
     attGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTgg                                                               >  1:1164402/3‑71 (MQ=255)
        gCGACTTGCCTCATGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTa                                                             >  1:1000755/1‑70 (MQ=255)
         cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTAc                                                            <  1:3645032/70‑1 (MQ=255)
         cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTAc                                                            <  1:1217644/70‑1 (MQ=255)
         cGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTat                                                            <  1:3768923/70‑2 (MQ=255)
             ttGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTc                                                       >  1:2335376/1‑71 (MQ=255)
               gCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTgg                                                               <  1:2292016/61‑1 (MQ=255)
               gCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTgg                                                               <  1:313955/61‑1 (MQ=255)
                cctcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCa                                                     >  1:1639362/1‑70 (MQ=255)
                  tcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCa                                                     <  1:2338139/68‑1 (MQ=255)
                  tcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCa                                                     <  1:2042996/68‑1 (MQ=255)
                    ctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAc                                                <  1:2468480/71‑1 (MQ=255)
                      gCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAcat                                              >  1:2493073/1‑71 (MQ=255)
                       cGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAcat                                              >  1:2353916/1‑70 (MQ=255)
                       cGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAca                                               <  1:3653117/69‑1 (MQ=255)
                        gTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAcatca                                            <  1:784003/71‑1 (MQ=255)
                        gTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAcatc                                             >  1:3764119/1‑70 (MQ=255)
                         tctcCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTgg                                                               <  1:971659/51‑1 (MQ=255)
                            ccGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCt                                                  >  1:2402554/1‑61 (MQ=255)
                            ccGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACatcatc                                          <  1:2893811/69‑1 (MQ=255)
                            ccGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGc                                        >  1:3814001/1‑71 (MQ=255)
                             cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATctgctg                                                                    <  1:678182/42‑1 (MQ=255)
                              gCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGc                                        >  1:907856/1‑69 (MQ=255)
                              gCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCt                                      <  1:700540/71‑1 (MQ=255)
                              gCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCt                                      <  1:844787/71‑1 (MQ=255)
                               cAAACCTGGGGCGAGCAAACTGACGTACCGTAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTg                                     <  1:1783589/71‑1 (MQ=255)
                               cAAACCTGGGGCGAGCAAACTGACGTACCGTAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTg                                     <  1:2627818/71‑1 (MQ=255)
                               cAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTg                                     >  1:457520/1‑71 (MQ=255)
                               atgaCCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTg                                     <  1:634745/68‑1 (MQ=255)
                                aaaCCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTgg                                    <  1:2405470/71‑1 (MQ=255)
                                aaaCCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTgg                                    >  1:224929/1‑71 (MQ=255)
                                aaaCCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTg                                     <  1:1740443/70‑1 (MQ=255)
                                 gaCCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTggg                                   >  1:2159452/2‑71 (MQ=255)
                                  aCCTGGGGCGAGCAAACTGACGTACCGGAATctgctg                                                                    <  1:1945852/37‑1 (MQ=255)
                                  aCCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACaa                                                          <  1:403347/47‑1 (MQ=255)
                                  aCCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTgggg                                  >  1:1181728/1‑71 (MQ=255)
                                  aCCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTgggg                                  <  1:216741/71‑1 (MQ=255)
                                    cTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTgggg                                  >  1:3310098/1‑69 (MQ=255)
                                     tGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGt                                >  1:2265544/1‑70 (MQ=255)
                                       gggCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCa                              <  1:3753141/70‑1 (MQ=255)
                                       gggCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCa                              <  1:3053453/70‑1 (MQ=255)
                                         gCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTat                                                            <  1:1616344/38‑2 (MQ=37)
                                         gCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTat                                                            <  1:2570036/38‑2 (MQ=37)
                                          cGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACg                          <  1:259794/71‑1 (MQ=255)
                                           gAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACg                          >  1:98572/1‑70 (MQ=255)
                                             gctaaCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGc                       <  1:1355083/68‑1 (MQ=255)
                                             gCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGc                       <  1:2662689/71‑1 (MQ=255)
                                              cAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGcc                      <  1:618696/71‑1 (MQ=255)
                                              cAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGcc                      >  1:1545580/1‑71 (MQ=255)
                                              cAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGcc                      <  1:1191578/71‑1 (MQ=255)
                                              cAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGc                       >  1:1217330/1‑70 (MQ=255)
                                               aaaCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                             <  1:2915844/63‑1 (MQ=255)
                                                aaCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGc                    <  1:3461661/71‑1 (MQ=255)
                                                aaCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGC‑ACATCATCGCCTGGGGGTCAAAc                           >  1:2568647/1‑63 (MQ=255)
                                                aaCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGC‑ACATCATCGCCTGGGGGTCAAAc                           >  1:2409408/1‑63 (MQ=255)
                                                 accgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                     >  1:2536065/4‑69 (MQ=255)
                                                 aCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCg                     >  1:2502871/1‑69 (MQ=255)
                                                     aCGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGa                 <  1:3652509/69‑1 (MQ=255)
                                                     aCGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGAc                <  1:3415441/70‑1 (MQ=255)
                                                       gTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTgggg                                  <  1:120462/50‑1 (MQ=38)
                                                       gTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGAcacg             <  1:2666827/71‑1 (MQ=255)
                                                        tACCGGAATCTGCTGACTGGTACAACTCCAGCTACatcatc                                          <  1:3269632/41‑1 (MQ=255)
                                                        tACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGt            <  1:225416/71‑1 (MQ=255)
                                                        tACCGGAATCTGCCGACTGGTATAACTCCAGCTACTTCATCGCCTGGGGGTCTAACGTACCGCAGAcac              <  1:228291/69‑3 (MQ=255)
                                                        tACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGAcacg             <  1:1049604/70‑1 (MQ=255)
                                                         aCCGGAATCTGCCGACTGGTATAACTCCAGCTAGATCATCGCCTGGGGGTCTAACGTACCGCAGACACGt            <  1:1323966/70‑1 (MQ=255)
                                                         aCCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTa           >  1:2342308/1‑71 (MQ=255)
                                                         aCCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTa           >  1:2193418/1‑71 (MQ=255)
                                                          ccGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGa                 <  1:3919279/64‑1 (MQ=255)
                                                          ccGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGAcacgaa           >  1:1522485/1‑68 (MQ=255)
                                                           cGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGt                                >  1:161398/1‑48 (MQ=255)
                                                           cGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcc         <  1:2679312/71‑1 (MQ=255)
                                                           cGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGAca               >  1:1701875/1‑64 (MQ=255)
                                                            ggAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAccc        >  1:3743391/1‑71 (MQ=255)
                                                             gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAcgcc       <  1:390411/71‑1 (MQ=255)
                                                              aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGTTCAAACGTGCCGCAGACGCGTACCCCg      <  1:485721/71‑1 (MQ=255)
                                                              aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCg      <  1:3692813/71‑1 (MQ=255)
                                                              aaTCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                 >  1:2412859/1‑60 (MQ=255)
                                                               aactgctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCa                   <  1:211184/55‑1 (MQ=255)
                                                                tCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTct                              <  1:188414/45‑2 (MQ=38)
                                                                  tgccgACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGacg  >  1:170482/1‑69 (MQ=255)
                                                                     tgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATg  <  1:887414/68‑1 (MQ=255)
                                                                     |                                                                   
CTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATG  >  minE/832199‑832335

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