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 386,425 C→G 8.0% N545K (AAC→AAG)  cstA → carbon starvation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE386,4250CG 8.0% 182.2 / 5.5 62N545K (AAC→AAG) cstAcarbon starvation protein
Reads supporting (aligned to +/- strand):  ref base C (26/31);  new base G (2/3);  total (28/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

GCTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGT  >  minE/386359‑386493
                                                                  |                                                                    
gcTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACActc                                                                  <  1:1992996/71‑1 (MQ=255)
    tgCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCtg                                                                <  1:1298947/69‑1 (MQ=255)
    tgCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCtg                                                                <  1:218731/69‑1 (MQ=255)
      cGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTgg                                                             <  1:2854286/70‑1 (MQ=255)
      cGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTgg                                                             <  1:3802474/70‑1 (MQ=255)
        tACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCg                                                          >  1:3546732/1‑71 (MQ=255)
            ggCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGt                                                      >  1:1572174/1‑71 (MQ=255)
            ggCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGt                                                      >  1:1556499/1‑71 (MQ=255)
             gCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGGGGCATTAACACTCTGTGGCCGCTGtt                                                     >  1:3860946/1‑71 (MQ=255)
             gCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGtt                                                     <  1:2578321/71‑1 (MQ=255)
             gCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGtt                                                     <  1:1008083/71‑1 (MQ=255)
             gCGGGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCtg                                                                <  1:2022494/60‑1 (MQ=255)
               gTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTg                                                   >  1:3422852/1‑71 (MQ=255)
                tGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTgg                                                  <  1:1384757/71‑1 (MQ=255)
                  gggCTACTTCCTCCATCATGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGt                                                 <  1:697887/70‑1 (MQ=255)
                  gggCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTa                                                >  1:633637/1‑71 (MQ=255)
                  gggCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCCGTGGCCGCTGtt                                                     <  1:42016/66‑1 (MQ=255)
                   ggCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCtgtg                                                              >  1:90581/1‑56 (MQ=255)
                    gCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAtt                                              <  1:1400524/71‑1 (MQ=255)
                      tacttactCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGtt                                                     >  1:2705529/1‑62 (MQ=255)
                      tACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGc                                            >  1:1419834/1‑71 (MQ=255)
                       aCTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCGGCTGTTTGGTATTGc                                            >  1:149171/1‑70 (MQ=255)
                       aCTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGc                                            >  1:3195728/1‑70 (MQ=255)
                       aCTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGc                                            >  1:141739/1‑70 (MQ=255)
                        cTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGcc                                           >  1:1986492/1‑70 (MQ=255)
                         ttCCTCCATCAGGGCGTGGTCGATCCGCCGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCaa                                         >  1:2960936/1‑71 (MQ=255)
                          tcctccATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCaa                                         >  1:2481852/1‑70 (MQ=255)
                              ccATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAAc                                        >  1:2955634/1‑67 (MQ=255)
                               cATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGAt                                   <  1:155986/71‑1 (MQ=255)
                                aTCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTAtct                                             >  1:3356265/1‑58 (MQ=255)
                                aTCAGGGCGTGGTCGATCCGCTTGGCGGCATTAACAct                                                                   <  1:1214192/38‑1 (MQ=255)
                                aTCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATg                                  <  1:665327/71‑1 (MQ=255)
                                 tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATg                                  <  1:1210251/70‑1 (MQ=255)
                                 tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGc                                 >  1:2737037/1‑71 (MQ=255)
                                 tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAAc                                        >  1:2183047/1‑64 (MQ=255)
                                 tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGc                                 <  1:2140766/71‑1 (MQ=255)
                                     ggCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGc                             <  1:452322/71‑1 (MQ=255)
                                      gCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTgg                                                  <  1:3584432/49‑1 (MQ=255)
                                      gCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTgg                                                  <  1:2442816/49‑1 (MQ=255)
                                        gTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCt                                <  1:1683315/65‑1 (MQ=19)
                                         tGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCaa                                         <  1:2982150/55‑1 (MQ=16)
                                         tGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAg                           <  1:2971277/69‑1 (MQ=255)
                                           gTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGa                        <  1:1116822/70‑1 (MQ=255)
                                            tCGATCCGCTGGGCGGCATTAACACTCTGTGGGCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATg                      >  1:205137/1‑71 (MQ=255)
                                            tCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATg                      >  1:1063233/1‑71 (MQ=255)
                                             cGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCt                                                        <  1:773005/36‑1 (MQ=255)
                                                tCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGgcgc                  <  1:2405604/71‑1 (MQ=255)
                                                tCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGgcgc                  <  1:83250/71‑1 (MQ=255)
                                                 ccGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt                 >  1:3128460/1‑71 (MQ=255)
                                                  cGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt                 <  1:347877/70‑1 (MQ=255)
                                                       ggcggcATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATg             <  1:435572/69‑1 (MQ=255)
                                                       ggcggcATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGc            <  1:1447753/70‑1 (MQ=255)
                                                         cggcATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGctct         >  1:2905870/1‑71 (MQ=255)
                                                             aTTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGAt                       >  1:961338/1‑53 (MQ=255)
                                                             aTTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGa               <  1:2797230/61‑1 (MQ=255)
                                                              ttAACACTCTGTGGCCGCTGTTTGGTATTGCCAAcc                                       <  1:2049916/36‑1 (MQ=255)
                                                               tAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCg   >  1:362669/1‑71 (MQ=255)
                                                               tAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCg   >  1:2927949/1‑71 (MQ=255)
                                                                aaCACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgt  >  1:3207140/1‑71 (MQ=255)
                                                                aaCACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgt  >  1:1287479/1‑71 (MQ=255)
                                                                aaCACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCg   <  1:3513592/70‑1 (MQ=255)
                                                                aaCACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCg   <  1:85649/70‑1 (MQ=255)
                                                                 acacTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGctct         >  1:3667578/1‑63 (MQ=255)
                                                                 acacTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGct           <  1:1234567/61‑1 (MQ=255)
                                                                 acacTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgt  <  1:85950/70‑1 (MQ=255)
                                                                  |                                                                    
GCTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGT  >  minE/386359‑386493

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