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 1,960,813 A→G 36.3% I212I (ATT→ATC)  pgk ← phosphoglycerate kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,960,8130AG36.3% 37.4 / 39.2 66I212I (ATT→ATC) pgkphosphoglycerate kinase
Reads supporting (aligned to +/- strand):  ref base A (33/9);  new base G (7/17);  total (40/26)
Fisher's exact test for biased strand distribution p-value = 1.66e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTTACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGA  >  minE/1960755‑1960875
                                                          |                                                              
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:1043693/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:99090/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:904296/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:874896/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:777629/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:623079/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:548997/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:437334/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:393127/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:2785346/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:2765651/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:2709144/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:2080666/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:189097/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:1735814/69‑1 (MQ=255)
aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:1145789/69‑1 (MQ=255)
   tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCt                                                         >  1:197121/1‑63 (MQ=255)
   tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                                    >  1:1813248/1‑68 (MQ=255)
   tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                                    >  1:605161/1‑68 (MQ=255)
   tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                                    >  1:3058186/1‑68 (MQ=255)
   tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                                    >  1:1489071/1‑68 (MQ=255)
   tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                                    >  1:267273/1‑68 (MQ=255)
   tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                                    >  1:2961781/1‑68 (MQ=255)
   tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                                    >  1:2956146/1‑68 (MQ=255)
   tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                                    >  1:2474848/1‑68 (MQ=255)
   tACCCACATCGTGGCCTTGTGACGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGt                                                      >  1:1925618/1‑66 (MQ=255)
           tCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTa                                           <  1:2709575/69‑1 (MQ=255)
           tCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTa                                           <  1:908313/69‑1 (MQ=255)
             gTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                                      <  1:1702365/56‑1 (MQ=255)
                   ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAggg                                    >  1:285083/1‑68 (MQ=255)
                   ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                                   >  1:1424405/1‑69 (MQ=255)
                   ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                                   >  1:2975565/1‑69 (MQ=255)
                   ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                                   >  1:3052192/1‑69 (MQ=255)
                   ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                                   >  1:1777995/1‑69 (MQ=255)
                   ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                                   >  1:2529121/1‑69 (MQ=255)
                   ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                                   >  1:1995758/1‑69 (MQ=255)
                                        aGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGttt                 >  1:1002837/1‑66 (MQ=255)
                                        aGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGttt                 >  1:631440/1‑66 (MQ=255)
                                        aGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGttt                 >  1:130658/1‑66 (MQ=255)
                                        aGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGttt                 >  1:2308715/1‑66 (MQ=255)
                                             tACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATa         <  1:1195986/69‑1 (MQ=255)
                                             tACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATa         >  1:2793772/1‑69 (MQ=255)
                                             tACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATa         >  1:883860/1‑69 (MQ=255)
                                             tACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATa         <  1:3434867/69‑1 (MQ=255)
                                             tACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATa         >  1:43097/1‑69 (MQ=255)
                                              accaccaccAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGt                                 >  1:3284400/1‑44 (MQ=255)
                                              accaccaccAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATAc        >  1:517214/1‑69 (MQ=255)
                                              accaccaccAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATAc        >  1:616076/1‑69 (MQ=255)
                                              accaccaccAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATAc        >  1:1319862/1‑69 (MQ=255)
                                              accaccaccAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATAc        >  1:1325881/1‑69 (MQ=255)
                                              accaccaccAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATAc        >  1:3318806/1‑69 (MQ=255)
                                               ccaccaccaACAATCAGCTGGTCAGCGATTTTAGTCAGGGAGTCCAGAACGGTCAGTTTGGTAGATAc        >  1:917296/1‑68 (MQ=255)
                                               ccaccaccaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATAc        >  1:2470789/1‑68 (MQ=255)
                                               ccaccaccaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATAc        >  1:648050/1‑68 (MQ=255)
                                               ccaccaccaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATAc        >  1:234479/1‑68 (MQ=255)
                                                    accaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTTGTAGATACTTTAg   >  1:2474642/1‑68 (MQ=255)
                                                    accaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  >  1:1581448/1‑69 (MQ=255)
                                                    accaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  >  1:1698660/1‑69 (MQ=255)
                                                    accaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  <  1:1093811/69‑1 (MQ=255)
                                                    accaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  >  1:2353247/1‑69 (MQ=255)
                                                    accaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  <  1:1669076/69‑1 (MQ=255)
                                                    accaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  >  1:585598/1‑69 (MQ=255)
                                                    accaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  >  1:3126573/1‑69 (MQ=255)
                                                    accaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  <  1:2389104/69‑1 (MQ=255)
                                                     ccaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  <  1:692805/68‑1 (MQ=255)
                                                     ccaACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGa  <  1:1206573/68‑1 (MQ=255)
                                                          |                                                              
ATTTACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTTGGTAGATACTTTAGA  >  minE/1960755‑1960875

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A