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 1,690,455 A→C 36.5% L389L (CTT→CTG)  hscA ← DnaK‑like molecular chaperone specific for IscU

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,690,4550AC36.5% 42.3 / 64.0 74L389L (CTT→CTG) hscADnaK‑like molecular chaperone specific for IscU
Reads supporting (aligned to +/- strand):  ref base A (19/28);  new base C (19/8);  total (38/36)
Fisher's exact test for biased strand distribution p-value = 1.66e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

ACGCGGAATCACTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCC  >  minE/1690389‑1690517
                                                                  |                                                              
aCGCGGAATCACTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCaa                                                               >  1:726919/1‑68 (MQ=255)
   cgGAATCACTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGc                                                             >  1:2751126/1‑67 (MQ=255)
      aaTCACTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAg                                                        <  1:932204/69‑1 (MQ=255)
      aaTCACTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAg                                                        <  1:735318/69‑1 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:2089211/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:2985316/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:3022060/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:2680402/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:243675/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:231213/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:2107631/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:625111/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:2019645/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:1850426/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:659763/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAtt                                                    >  1:708358/1‑69 (MQ=255)
          aCTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCAt                                                     >  1:2876435/1‑68 (MQ=255)
                 ccaccaGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTg                                              <  1:1690079/68‑1 (MQ=255)
                 ccaccaGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTg                                              <  1:2935794/68‑1 (MQ=255)
                 ccaccaGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTg                                              <  1:1502747/68‑1 (MQ=255)
                 ccaccaGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTg                                              <  1:2818700/68‑1 (MQ=255)
                 ccaccaGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTg                                              <  1:372941/68‑1 (MQ=255)
                 ccaccaGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTg                                              <  1:3138308/68‑1 (MQ=255)
                 ccaccaGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTg                                              <  1:1331762/68‑1 (MQ=255)
                              cATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                <  1:1756529/69‑1 (MQ=255)
                              cATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                <  1:2865068/69‑1 (MQ=255)
                              cATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                <  1:123153/69‑1 (MQ=255)
                              cATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                <  1:2312864/69‑1 (MQ=255)
                               aTCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                <  1:2281996/68‑1 (MQ=255)
                               aTCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                <  1:852163/68‑1 (MQ=255)
                                  gTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAccc                               >  1:1007978/1‑66 (MQ=255)
                                  gTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAccc                               >  1:3312450/1‑66 (MQ=255)
                                  gTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAccc                               >  1:604020/1‑66 (MQ=255)
                                       gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                        <  1:819569/68‑1 (MQ=255)
                                       gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                        <  1:2514860/68‑1 (MQ=255)
                                       gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                        <  1:2723011/68‑1 (MQ=255)
                                       gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                        <  1:760250/68‑1 (MQ=255)
                                       gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                        <  1:1201769/68‑1 (MQ=255)
                                       gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                        <  1:645925/68‑1 (MQ=255)
                                       gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                        <  1:1653558/68‑1 (MQ=255)
                                       gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                        <  1:701922/68‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:3273610/69‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:3199050/69‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:3294481/69‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:1010089/69‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:2337681/69‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:1182647/69‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:2317794/69‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:1707408/69‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:1786145/69‑1 (MQ=255)
                                                 gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:2131405/69‑1 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAata                      >  1:751751/1‑60 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:2044506/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:985099/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:956581/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:137425/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:1417889/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:1452255/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:717512/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:1764025/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:1806149/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:2039060/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:2849937/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:590288/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:488317/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:426950/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:2284396/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:2307900/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:2680290/1‑69 (MQ=255)
                                                 gACAGCGGGATCACATCCAGAAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa             >  1:1261635/1‑69 (MQ=255)
                                                  aCAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:2221740/68‑1 (MQ=255)
                                                  aCAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa             <  1:3136759/68‑1 (MQ=255)
                                                      tGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATcgc        >  1:360649/1‑69 (MQ=255)
                                                      tGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATcgc        >  1:3272479/1‑69 (MQ=255)
                                                            cacaTCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCTACCAGAATATCCGCCTGAATCGCCGCGcc  <  1:516232/69‑1 (MQ=255)
                                                                  |                                                              
ACGCGGAATCACTTTCTCCACCAGGCCGCCCATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCC  >  minE/1690389‑1690517

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A