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
A4 F28 I1 R1 100 74.7 2540932 99.2% 2520604 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,428,499 G→C A76A (GCC→GCG)  insH‑5 ← Rac prophage; IS5 transposase and trans‑activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,428,4990GC100.0% 158.7 / NA 46A76A (GCC→GCG) insH‑5Rac prophage; IS5 transposase and trans‑activator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (22/24);  total (22/24)

CCGGCAGGGCGCTATCCAGGGATAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGGGCATCTTCCATGGCACCGTCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGCCATGGCA  >  NC_000913/1428426‑1428632
                                                                         |                                                                                                                                     
ccGGCAAGGCGCTATCCAGGGATAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAg                                                                     >  2:836615/1‑140 (MQ=11)
ccGGCAAGGCGCTATCCAGGGATAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAg                                                                     >  1:1241307/1‑140 (MQ=11)
      aggCGCTATCCAGGGATAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGt                                                               <  2:477392/139‑1 (MQ=255)
         cgcTATCCAGGGATAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGt                                                               <  2:251120/137‑1 (MQ=255)
         cgcTATCCAGGGATAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGt                                                               >  1:251120/1‑137 (MQ=255)
         cgcTATCCAGGGATAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCgg                                                            <  1:1082904/140‑1 (MQ=255)
                  gggATAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGccc                                                   >  1:622708/1‑140 (MQ=255)
                     aTAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGcc                                                <  1:837390/140‑1 (MQ=255)
                      tAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCt                                               <  1:699680/140‑1 (MQ=255)
                      tAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCt                                               <  1:580899/140‑1 (MQ=255)
                        aTCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTg                                             >  2:775258/1‑140 (MQ=255)
                        aTCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTg                                             >  1:853985/1‑140 (MQ=255)
                        aTCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTg                                             >  1:694092/1‑140 (MQ=255)
                        aTCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTg                                             >  2:373817/1‑140 (MQ=255)
                        aTCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTg                                             >  2:611007/1‑140 (MQ=255)
                           gggCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGTGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGa                                          <  2:773885/140‑1 (MQ=14)
                            ggCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGc                                                           <  2:347143/122‑1 (MQ=255)
                            ggCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGc                                                           >  1:347143/1‑122 (MQ=255)
                             gCAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATa                                        >  1:625096/1‑140 (MQ=255)
                              cAAACAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATaa                                       >  1:64093/1‑140 (MQ=255)
                               aaaCAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATaaa                                      >  1:518481/1‑140 (MQ=255)
                               aaaCAGACGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCt                                               >  2:130522/1‑131 (MQ=11)
                               aaaCAGACGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCt                                               <  1:130522/131‑1 (MQ=14)
                                 aCAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAAc                                    <  1:311307/140‑1 (MQ=255)
                                 aCAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAAc                                    >  2:311307/1‑140 (MQ=255)
                                 aCAGGCGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAAc                                    >  1:596913/1‑140 (MQ=255)
                                          tGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATg                           <  1:240324/140‑1 (MQ=255)
                                            gAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGAc                         <  2:625096/140‑1 (MQ=255)
                                            gAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGAc                         <  1:371008/140‑1 (MQ=255)
                                             aGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACa                        <  2:546276/140‑1 (MQ=255)
                                              ggCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAg                       <  1:874854/140‑1 (MQ=255)
                                              ggCGATTTCGTACAGAGCATCGTCCATCGCGCCTTCGCTCAGGTTGTTCCAATGCGGCAGGCAGTGAATTCGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATGGCCCGCCTTGGGATAAAACGGCTCGATGACAg                       <  2:269117/140‑1 (MQ=14)
                                                  aTTTCGTACAGAGCATCTTGCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCGGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGt                   <  2:613111/140‑1 (MQ=14)
                                                  aTTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGt                   <  2:375981/140‑1 (MQ=255)
                                                   tttCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTc                  <  1:836615/140‑1 (MQ=255)
                                                     tCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCat                >  2:473521/1‑140 (MQ=17)
                                                       gTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCatat              <  1:373817/140‑1 (MQ=255)
                                                            gagCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGc         >  2:453273/3‑140 (MQ=255)
                                                            gagCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGc         >  1:1090421/3‑140 (MQ=17)
                                                             agCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGcc        >  2:759194/2‑140 (MQ=255)
                                                             agCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGcc        <  1:759194/139‑1 (MQ=255)
                                                             agCATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGcc        <  2:104538/139‑1 (MQ=255)
                                                               cATCTTCCATCGCGCCATCGCTCGGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGCCAt      >  1:1027679/1‑140 (MQ=18)
                                                               cATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGCCAt      >  1:1085112/1‑140 (MQ=255)
                                                               cATCTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGCCAt      <  2:154213/140‑1 (MQ=255)
                                                                  cTTCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGCCATGGc   <  2:622708/140‑1 (MQ=255)
                                                                   ttCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGCCATGGCa  <  1:836783/140‑1 (MQ=255)
                                                                   ttCCATCGCGCCATCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGCCATGGCa  <  2:751612/140‑1 (MQ=255)
                                                                         |                                                                                                                                     
CCGGCAGGGCGCTATCCAGGGATAATCGGGCAAACAGGCGCATGGAGGCGATTTCGTACAGGGCATCTTCCATGGCACCGTCGCTCAGGTTGTACCAATGCTGCATGCAGTGAATACGCAGCATGGTCTCCAGCGGATAGGGCCGTCGGCCATTGCCCGCCTTGGGATAAAACGGCTCGATGACAGCGGTCATATTCTGCCATGGCA  >  NC_000913/1428426‑1428632

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A