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 2,317,744 G→A 32.3% P104P (CCG→CCA)  fpr → ferredoxin‑NADP reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,317,7440GA32.3% 60.2 / 34.5 71P104P (CCG→CCA) fprferredoxin‑NADP reductase
Reads supporting (aligned to +/- strand):  ref base G (27/21);  new base A (14/9);  total (41/30)
Fisher's exact test for biased strand distribution p-value = 8.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.22e-01

GAAACCAGGCGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCGATTCTGC  >  minE/2317678‑2317808
                                                                  |                                                                
gAAACCAGGCGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCa                                                                >  1:2523455/1‑69 (MQ=255)
gAAACCAGGCGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCa                                                                >  1:3197309/1‑69 (MQ=255)
gAAACCAGGCGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCa                                                                >  1:2512713/1‑69 (MQ=255)
gAAACCAGGCGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCa                                                                >  1:2288971/1‑69 (MQ=255)
gAAACCAGGCGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCa                                                                >  1:3436494/1‑69 (MQ=255)
gAAACCAGGCGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCa                                                                >  1:1135383/1‑69 (MQ=255)
gAAACCAGGCGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCa                                                                >  1:274144/1‑69 (MQ=255)
      gggCGATGAAGTGCAGGTGGTTAGCGAAGCCGCTGGCTTCTTTGTGCTGGATGAAGTACCAGATTGCGa                                                          <  1:3264720/68‑1 (MQ=255)
      gggCGATGAAGTGCAGGTGGTTAGCGAAGCCGCTGGCTTCTTTGTGCTGGATGAAGTACCAGATTGCGa                                                          <  1:710110/68‑1 (MQ=255)
      gggCGATGAAGTGCAGGTGGTTAGCGAAGCCGCTGGCTTCTTTGTGCTGGATGAAGTACCAGATTGCGa                                                          <  1:733926/68‑1 (MQ=255)
      gggCGATGAAGTGCAGGTGGTTAGCGAAGCCGCTGGCTTCTTTGTGCTGGATGAAGTACCAGATTGCGa                                                          <  1:1901447/68‑1 (MQ=255)
      gggCGATGAAGTGCAGGTGGTTAGCGAAGCCGCTGGCTTCTTTGTGCTGGATGAAGTACCAGATTGCGa                                                          <  1:1846819/68‑1 (MQ=255)
      gggCGATGAAGTGCAGGTGGTTAGCGAAGCCGCTGGCTTCTTTGTGCTGGATGAAGTACCAGATTGCGa                                                          <  1:3041359/68‑1 (MQ=255)
      gggCGATGAAGTGCAGGTGGTTAGCGAAGCCGCTGGCTTCTTTGTGCTGGATGAAGTACCAGATTGCGa                                                          <  1:1247931/68‑1 (MQ=255)
      gggCGATGAAGTGCAGGTGGCTAGCGAAGCCGCTGGCTTCTTTGTGCTGGATGAAGTACCAGATTGCGa                                                          <  1:75047/68‑1 (MQ=255)
       ggCGATGAAGTGCAGGTGGTTAGCGAAGCCGCTGGCTTCTTTGTGCTGGATGAAGTACCAGATTGCGa                                                          <  1:2523764/68‑1 (MQ=255)
         cGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAAc                                                       >  1:1876560/1‑69 (MQ=255)
         cGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAAc                                                       >  1:2039964/1‑69 (MQ=255)
            tGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCt                                                    <  1:1563802/69‑1 (MQ=255)
            tGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCt                                                    <  1:1503807/69‑1 (MQ=255)
            tGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCt                                                    <  1:2608089/69‑1 (MQ=255)
             gAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCt                                                    <  1:281793/68‑1 (MQ=255)
             gAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCt                                                    <  1:2450978/68‑1 (MQ=255)
             gAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTa                                                   >  1:3365108/1‑69 (MQ=255)
             gAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTa                                                   >  1:364650/1‑69 (MQ=255)
             gAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTa                                                   >  1:2511380/1‑69 (MQ=255)
             gAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTa                                                   >  1:456524/1‑69 (MQ=255)
             gAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTa                                                   >  1:2674626/1‑69 (MQ=255)
             gAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTa                                                   >  1:1930428/1‑69 (MQ=255)
             gAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTa                                                   >  1:3425166/1‑69 (MQ=255)
                    aGGTGGTTAGCGTAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCt                                                    <  1:1818690/61‑1 (MQ=255)
                      gtggtTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCta                                          >  1:1239779/1‑68 (MQ=255)
                           tAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAAc                                     >  1:886427/1‑69 (MQ=255)
                                    ggCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            <  1:2698514/69‑1 (MQ=255)
                                    ggCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            <  1:1149380/69‑1 (MQ=255)
                                    ggCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            <  1:387247/69‑1 (MQ=255)
                                    ggCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            <  1:1559431/69‑1 (MQ=255)
                                       aGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATg                                                 <  1:1499135/45‑1 (MQ=255)
                                          aTTCTTTGTGCTCTATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTgg                      >  1:2514598/1‑69 (MQ=255)
                                          aTTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCgg                                  <  1:2548180/57‑1 (MQ=255)
                                          aTTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCgg                                  <  1:742300/57‑1 (MQ=255)
                                          aTTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCgg                                  <  1:1919447/57‑1 (MQ=255)
                                             cTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCg                           >  1:2567601/1‑61 (MQ=255)
                                             cTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCg                           >  1:1894838/1‑61 (MQ=255)
                                             cTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCg                           >  1:1291963/1‑61 (MQ=255)
                                             cTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCg                           >  1:1279938/1‑61 (MQ=255)
                                             cTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCg                           >  1:1231440/1‑61 (MQ=255)
                                             cTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCg                           >  1:3299844/1‑61 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:384262/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:626789/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:926004/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:1548701/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:3014651/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:2807122/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:2731928/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:2542460/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:2452583/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:2401939/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:1932162/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:2240108/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:2136621/1‑58 (MQ=255)
                                               ttGTGCTGGATGAAGTACCAGATTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            >  1:2021070/1‑58 (MQ=255)
                                                         tGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCGAt       <  1:612112/69‑1 (MQ=255)
                                                         tGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCGAt       <  1:1785803/69‑1 (MQ=255)
                                                         tGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCGAt       <  1:794440/69‑1 (MQ=255)
                                                         tGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCGAt       <  1:2040007/69‑1 (MQ=255)
                                                         tGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCGAt       <  1:3229167/69‑1 (MQ=255)
                                                         tGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCGAt       <  1:2540946/69‑1 (MQ=255)
                                                          gAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCg         >  1:331682/1‑66 (MQ=255)
                                                              tGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCGATTCTGc  >  1:898856/1‑69 (MQ=255)
                                                               gCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGc                            <  1:452083/42‑1 (MQ=255)
                                                                  |                                                                
GAAACCAGGCGATGAAGTGCAGGTGGTTAGCGAAGCGGCAGGATTCTTTGTGCTCGATGAAGTGCCGCACTGCGAAACGCTATGGATGCTGGCAACCGGTACAGCGATTGGCCCTTATTTATCGATTCTGC  >  minE/2317678‑2317808

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