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 677,923 C→T 71.1% G29G (GGC→GGT)  yccR → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE677,9230CT71.1% 136.8 / 64.4 138G29G (GGC→GGT) yccRconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/17);  new base T (37/61);  total (60/78)
Fisher's exact test for biased strand distribution p-value = 3.89e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.63e-01

Only 100 of 142 total aligned reads displayed.

AGCGGATCTATAAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGT  >  minE/677856‑677981
                                                                   |                                                          
aGCGGATCTATAAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGc                                                            <  1:1103519/68‑1 (MQ=255)
  cGGATCTATAAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGt                                                         <  1:958655/69‑1 (MQ=255)
  cGGATCTATAAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGt                                                         >  1:428513/1‑69 (MQ=255)
  cGGATCTATAAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGt                                                         >  1:2264411/1‑69 (MQ=255)
  cGGATCTATAAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGt                                                         >  1:1387425/1‑69 (MQ=255)
          taAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCt                                                 >  1:1018834/1‑69 (MQ=255)
          taAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCt                                                 >  1:1032952/1‑69 (MQ=255)
          taAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCt                                                 >  1:3059987/1‑69 (MQ=255)
            aaTCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTg                                                <  1:3171062/68‑1 (MQ=255)
            aaTCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTg                                                <  1:3150081/68‑1 (MQ=255)
              tCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGAcc                                             <  1:3289989/69‑1 (MQ=255)
              tCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGAcc                                             <  1:118037/69‑1 (MQ=255)
                acaAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCg                                            >  1:1051769/1‑68 (MQ=255)
                     aaTACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGtt                                          <  1:2357204/65‑1 (MQ=255)
                       tACCTGGCAACGTTGTGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:1265217/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAg                                                          >  1:260982/1‑47 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:1994249/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:66966/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:1117324/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:136114/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:3109745/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:554363/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:502709/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:298588/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:454690/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:1641520/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:1677310/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:374926/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:3300515/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:3183158/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGt                                                         >  1:1058385/1‑48 (MQ=255)
                       tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTgacgac                                    <  1:2580633/69‑1 (MQ=255)
                        aCCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGc                                                            <  1:3083217/44‑1 (MQ=255)
                         ccTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGacac                                  >  1:2209405/1‑69 (MQ=255)
                         ccTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGacac                                  >  1:2562261/1‑69 (MQ=255)
                         ccTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGacac                                  >  1:1235563/1‑69 (MQ=255)
                         catGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGacac                                  >  1:2826625/3‑69 (MQ=255)
                             gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                              >  1:471221/1‑69 (MQ=255)
                             gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                              >  1:2139204/1‑69 (MQ=255)
                             gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                              >  1:289027/1‑69 (MQ=255)
                             gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                              >  1:615272/1‑69 (MQ=255)
                             gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                              >  1:1173402/1‑69 (MQ=255)
                             gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                              >  1:1351293/1‑69 (MQ=255)
                             gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                              >  1:243331/1‑69 (MQ=255)
                             gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                              >  1:2463603/1‑69 (MQ=255)
                                     gggCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGAt                      <  1:2820844/69‑1 (MQ=255)
                                     gggCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGAt                      <  1:1247838/69‑1 (MQ=255)
                                     gggCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGAt                      <  1:2207475/69‑1 (MQ=255)
                                     gggAACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGAt                      >  1:3135723/1‑69 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:1617559/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:2042723/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:3067511/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:2496590/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:1051599/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:2104386/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:3425544/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:373572/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:502511/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:1189086/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:1214382/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:751498/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:2613474/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:91986/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:92382/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                         <  1:1017327/40‑1 (MQ=255)
                                               gAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGa             >  1:836989/1‑68 (MQ=255)
                                               gAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGa             >  1:3244962/1‑68 (MQ=255)
                                               gAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGAt            >  1:1855575/1‑69 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:2483708/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:2696808/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:804239/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:2614079/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:3426578/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:3368549/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:3334038/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:1846952/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:2422850/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:941724/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:1074588/69‑1 (MQ=255)
                                                         cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGATGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:3123514/69‑1 (MQ=255)
                                                         cATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:1979010/69‑1 (MQ=255)
                                                         cATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:1685152/69‑1 (MQ=255)
                                                         cATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:1038007/69‑1 (MQ=255)
                                                         cATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:2623667/69‑1 (MQ=255)
                                                          aTTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:3017154/68‑1 (MQ=255)
                                                          aTTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt  <  1:1000490/68‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:910043/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:2629729/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:1377331/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:226217/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:518325/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:1389736/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:2381290/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:1559086/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:2932008/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:2981321/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:1075867/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:3061720/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:3180586/45‑1 (MQ=255)
                                                               ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                    <  1:1985638/45‑1 (MQ=255)
                                                                   |                                                          
AGCGGATCTATAAATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGT  >  minE/677856‑677981

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A