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 1,125,725 A→G 48.9% T303T (ACT→ACC)  pheS ← phenylalanine tRNA synthetase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,125,7250AG48.9% ‑5.8 / 81.8 88T303T (ACT→ACC) pheSphenylalanine tRNA synthetase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (26/19);  new base G (22/21);  total (48/40)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

TGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGT  >  minE/1125664‑1125789
                                                             |                                                                
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGa                                                            >  1:412437/1‑68 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:3111952/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:2155064/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:226183/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:2022187/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:2317525/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:2996065/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:1955445/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:627611/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:299612/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:3029328/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:3170654/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:1526216/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:3184068/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:3216498/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:2621510/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:2841219/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:27006/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:2828488/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:564741/1‑69 (MQ=255)
tGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:2786973/1‑69 (MQ=255)
tGAGGAAACGCAGATCATTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGAc                                                           >  1:3338457/1‑69 (MQ=255)
        cGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatc                                                   <  1:525297/69‑1 (MQ=255)
        cGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatc                                                   <  1:2571930/69‑1 (MQ=255)
        cGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatc                                                   <  1:3400732/69‑1 (MQ=255)
        cGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatc                                                   <  1:508297/69‑1 (MQ=255)
        cGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatc                                                   <  1:1624027/69‑1 (MQ=255)
        cGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatc                                                   <  1:551802/69‑1 (MQ=255)
              tCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatccccatc                                             >  1:1346559/1‑69 (MQ=255)
              tCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatccccatc                                             >  1:3297231/1‑69 (MQ=255)
              tCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatccccatc                                             >  1:2598896/1‑69 (MQ=255)
              tCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTccatccccatc                                             >  1:1785212/1‑69 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAAGGCAACATAGTCAGACGCTc                                                       >  1:2296056/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTc                                                       >  1:3346554/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTc                                                       >  1:3335143/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTc                                                       >  1:2411361/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTc                                                       >  1:1849854/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTc                                                       >  1:1999637/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTc                                                       >  1:2324649/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTc                                                       >  1:2013815/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTc                                                       >  1:22909/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTc                                                       >  1:2287243/1‑58 (MQ=255)
               cGTTTTCGAAGAATGAACGCAGGTCGGTGACGACGTAACGCAACATAGTCAGACGCTc                                                       >  1:2551757/1‑58 (MQ=255)
                        agaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGa                                   <  1:40073/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:3277515/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:1141196/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:381827/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:555626/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:1431942/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:145297/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:1479591/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:1517380/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:1612092/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:540427/69‑1 (MQ=255)
                         gaaTGAACGCAGGTCGGTGACACCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGaa                                  <  1:3358687/69‑1 (MQ=255)
                           aTGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGATGGCGaa                                  <  1:436025/67‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:177201/69‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:3119907/69‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:2978182/69‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:2945251/69‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:3240534/69‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:2399644/69‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:2413618/69‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:40077/69‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:1385260/69‑1 (MQ=255)
                             gAACGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:377341/69‑1 (MQ=255)
                              aaCGCAGGTCGGTGACGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:1570916/68‑1 (MQ=255)
                                       cGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACtt                    >  1:593136/1‑69 (MQ=255)
                                       cGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACtt                    >  1:2666897/1‑69 (MQ=255)
                                       cGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACtt                    >  1:1773534/1‑69 (MQ=255)
                                           gACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCgg                >  1:2591436/1‑69 (MQ=255)
                                           gACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCgg                >  1:1308503/1‑69 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:648370/53‑1 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:381075/53‑1 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:105785/53‑1 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:2688257/53‑1 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:2360571/53‑1 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:484166/53‑1 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:2194089/53‑1 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:2037749/53‑1 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:1728311/53‑1 (MQ=255)
                                             cGCCGTAACGCAACATGGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCa                              <  1:1391992/53‑1 (MQ=255)
                                                         aCATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGt  >  1:90434/1‑69 (MQ=255)
                                                         aCATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGt  >  1:2701055/1‑69 (MQ=255)
                                                         aCATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGt  >  1:2865958/1‑69 (MQ=255)
                                                         aCATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGt  >  1:2849043/1‑69 (MQ=255)
                                                         aCATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGt  >  1:2713490/1‑69 (MQ=255)
                                                         aCATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCAGGGTCGATGCCAACGt  >  1:973622/1‑69 (MQ=255)
                                                             |                                                                
TGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGT  >  minE/1125664‑1125789

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