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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,251,656 G→A 25.5% intergenic (+4/+406) thiH → / ← htrC thiamin biosynthesis ThiGH complex subunit/heat shock protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,251,6560GA25.5% 94.1 / 26.6 78intergenic (+4/+406)thiH/htrCthiamin biosynthesis ThiGH complex subunit/heat shock protein
Reads supporting (aligned to +/- strand):  ref base G (38/20);  new base A (9/11);  total (47/31)
Fisher's exact test for biased strand distribution p-value = 1.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.02e-01

GGTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTT  >  minE/2251590‑2251716
                                                                  |                                                            
ggTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:276196/68‑1 (MQ=255)
ggTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:2603209/68‑1 (MQ=255)
ggTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:2070815/68‑1 (MQ=255)
ggTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:1829690/68‑1 (MQ=255)
ggTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:3102125/68‑1 (MQ=255)
ggTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:1599763/68‑1 (MQ=255)
ggTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:1128472/68‑1 (MQ=255)
ggTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:1398720/68‑1 (MQ=255)
ggTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:1217639/68‑1 (MQ=255)
 gTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACgg                                                             <  1:57069/67‑1 (MQ=255)
               tGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACGGAATGTAAGAACGTaaa                                             >  1:3173031/1‑69 (MQ=255)
               tGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACGGAATGTAAGAACGTaa                                              >  1:1242295/1‑68 (MQ=255)
                 gAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAAtt                                           >  1:1742236/1‑69 (MQ=255)
                    aGACTGGGACAGCTATCTGGGTCGCCCATGGCAAAGGCCATGAGACAGTATGTAAGAACGTAAATTTAt                                        <  1:2339711/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:2544968/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:2147340/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:1677703/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:907724/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:361069/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:2661622/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:1385935/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:3193288/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:1348890/69‑1 (MQ=255)
                    aGACTGGGACAGCTATCTGGGACGCCCATCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTAt                                        <  1:969695/69‑1 (MQ=255)
                            aCAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACGGAATGTAAGAACGTa                                               <  1:219332/54‑1 (MQ=255)
                             cAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACGGAATGTAAGAACGTa                                               <  1:1475545/53‑1 (MQ=255)
                                            cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                >  1:308216/1‑69 (MQ=255)
                                            cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                >  1:3380532/1‑69 (MQ=255)
                                            cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                >  1:207015/1‑69 (MQ=255)
                                            cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                >  1:2945229/1‑69 (MQ=255)
                                            cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                >  1:825059/1‑69 (MQ=255)
                                            cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                >  1:1344070/1‑69 (MQ=255)
                                            cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                >  1:173149/1‑69 (MQ=255)
                                            cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                >  1:594730/1‑69 (MQ=255)
                                              ccTAGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaaaa              <  1:3315495/69‑1 (MQ=255)
                                               cTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaaaa              <  1:2522185/68‑1 (MQ=255)
                                                tCGCAAAGGCCATGAGACAGATTGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc             >  1:109259/1‑68 (MQ=255)
                                                tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGaaaaa              >  1:1633103/1‑67 (MQ=255)
                                                tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc             >  1:1179340/1‑68 (MQ=255)
                                                tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc             >  1:2677497/1‑68 (MQ=255)
                                                tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc             >  1:2000144/1‑68 (MQ=255)
                                                tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc             >  1:771131/1‑68 (MQ=255)
                                                tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc             >  1:115722/1‑68 (MQ=255)
                                                tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc             >  1:664937/1‑68 (MQ=255)
                                                gcGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc             >  1:3118939/2‑68 (MQ=255)
                                                 cGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAAc             >  1:3134089/1‑67 (MQ=255)
                                                    aaaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGcc                                <  1:876554/45‑1 (MQ=255)
                                                    aaaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGcc                                <  1:574854/45‑1 (MQ=255)
                                                    aaaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGcc                                <  1:101701/45‑1 (MQ=255)
                                                    aaaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGcc                                <  1:920200/45‑1 (MQ=255)
                                                    aaaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGc                                 <  1:1194116/44‑1 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTcc                                     >  1:1735797/1‑39 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCg                                    >  1:1758718/1‑40 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACTGAAGATGAAAAACGCAAgg       >  1:97365/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:102148/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:355004/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:1023693/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:3349693/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:1305405/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:1641012/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:1698339/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:3069304/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:1871742/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:887197/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg       >  1:579835/1‑69 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg        >  1:3067248/1‑68 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg        >  1:303876/1‑68 (MQ=255)
                                                     aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg        >  1:106152/1‑68 (MQ=255)
                                                       gACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg        >  1:1008803/1‑66 (MQ=255)
                                                        aCTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg        >  1:279425/1‑65 (MQ=255)
                                                        aCTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGgttg    >  1:275504/1‑69 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        <  1:993033/47‑1 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        <  1:952811/47‑1 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        >  1:3229292/1‑47 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        <  1:3111556/47‑1 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        >  1:2997378/1‑47 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        >  1:2924156/1‑47 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        <  1:2649076/47‑1 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        <  1:260070/47‑1 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        >  1:1566909/1‑47 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        <  1:1494157/47‑1 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        >  1:1281199/1‑47 (MQ=255)
                                                          tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                        <  1:1101626/47‑1 (MQ=255)
                                                            tGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGgttgtt  >  1:147443/1‑67 (MQ=255)
                                                              agaCGGAATGTAAGAACGTAAATTTATTCCGAGcc                                <  1:574474/35‑1 (MQ=255)
                                                              agaCGGAATGTAAGAACGTAAATTTATTCCGAGcc                                <  1:3250076/35‑1 (MQ=255)
                                                              agaCGGAATGTAAGAACGTAAATTTATTCCGAGcc                                <  1:643455/35‑1 (MQ=255)
                                                              agaCGGAATGTAAGAACGTAAATTTATTCCGAGcc                                <  1:764955/35‑1 (MQ=255)
                                                                  |                                                            
GGTTTGCAGCCGGTATGGAAAGACTGGGACAGCTATCTGGGACGCGCCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTT  >  minE/2251590‑2251716

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