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 2,428,430 C→T 35.8% A17A (GCG→GCA)  rffE ← UDP‑N‑acetyl glucosamine‑2‑epimerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,428,4300CT35.8% 70.4 / 61.4 103A17A (GCG→GCA) rffEUDP‑N‑acetyl glucosamine‑2‑epimerase
Reads supporting (aligned to +/- strand):  ref base C (25/41);  new base T (17/20);  total (42/61)
Fisher's exact test for biased strand distribution p-value = 5.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 103 total aligned reads displayed.

TGCTGCGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATTCTCTT  >  minE/2428365‑2428492
                                                                 |                                                              
tgctgcGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGcc                                                             <  1:2176683/69‑1 (MQ=255)
tgctgcGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGcc                                                             <  1:1157413/69‑1 (MQ=255)
tgctgcGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGcc                                                             <  1:2760505/69‑1 (MQ=255)
tgctgcGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGcc                                                             <  1:2756353/69‑1 (MQ=255)
tgctgcGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGcc                                                             <  1:159554/69‑1 (MQ=255)
 gctgcGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGcc                                                             <  1:51616/68‑1 (MQ=255)
  ctgcGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCAt                                                           >  1:2212879/1‑69 (MQ=255)
  ctgcGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCAt                                                           >  1:3161472/1‑69 (MQ=255)
  ctgcGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCAt                                                           >  1:323552/1‑69 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACTGCGCCATCtt                                                        <  1:1777005/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:2750344/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:1067181/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:1951925/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:2603943/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:2493944/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:239166/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:3100443/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:2874521/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:3011713/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:3333727/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:356076/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:486791/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:1252640/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:846045/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:1217014/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:1096646/67‑1 (MQ=255)
       cAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:106719/67‑1 (MQ=255)
        aGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:2690510/66‑1 (MQ=255)
           gACGCAAACTTTAGCCTCTAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGc                                                  >  1:2690547/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:2009179/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:1675666/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:1640728/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:1968937/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:2513561/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:1984969/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:1630472/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:2934224/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:2480760/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:1444089/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:2368368/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:64876/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:767938/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:2182244/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:2803249/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGc                                                  >  1:2170230/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATATTGATGGc                                                  >  1:594644/1‑69 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        >  1:288964/1‑63 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        >  1:1921923/1‑63 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        >  1:2162607/1‑63 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        >  1:3163440/1‑63 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        >  1:527258/1‑63 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        >  1:656417/1‑63 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        >  1:843464/1‑63 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        >  1:883178/1‑63 (MQ=255)
           gACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        >  1:2675232/1‑63 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGTATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCt                                                 >  1:1468573/1‑69 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCt                                                 <  1:2241851/69‑1 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCt                                                 <  1:2141046/69‑1 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCt                                                 >  1:2342375/1‑69 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCt                                                 <  1:139221/69‑1 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCt                                                 >  1:2899054/1‑69 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCt                                                 >  1:1250355/1‑69 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCt                                                 <  1:2641750/69‑1 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCt                                                 <  1:3249934/69‑1 (MQ=255)
            aCGCAAACTTTAGCCTCAAAAAAAGGATCTTTTG‑CAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:276662/69‑1 (MQ=255)
              gCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:1922313/68‑1 (MQ=255)
              gCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:2405436/68‑1 (MQ=255)
              gCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:436509/68‑1 (MQ=255)
              gCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:3396399/68‑1 (MQ=255)
              gCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:792106/68‑1 (MQ=255)
              gCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:850573/68‑1 (MQ=255)
              gCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:2085245/68‑1 (MQ=255)
              gCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:1927900/68‑1 (MQ=255)
              gCAAACTTTAGCCTCAAAAAAAGGAGCTTTTGCCAACGCATGCACCAACGGTGCCATCTTGATGGCtt                                                <  1:2444449/68‑1 (MQ=255)
                   cTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCtt                                                        <  1:2862063/55‑1 (MQ=255)
                               aaaaaGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCaaa                                <  1:1769376/67‑1 (MQ=255)
                                         ttttGCCAACGCATGCACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCaaa                                <  1:699705/57‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTcaca             <  1:2483290/66‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTcaca             <  1:2870447/66‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTcaca             <  1:452179/66‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTcaca             <  1:425453/66‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTcaca             <  1:3420340/66‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTcaca             <  1:2939015/66‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTcaca             <  1:72776/66‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTcaca             <  1:3321342/66‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTcaca             <  1:2067848/66‑1 (MQ=255)
                                                   gCATGCACCAACGGTGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACGTTcaca             <  1:7626/66‑1 (MQ=255)
                                                      tGCACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGAtt       >  1:1830743/1‑69 (MQ=255)
                                                       gCACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATtc      <  1:597965/69‑1 (MQ=255)
                                                       gCACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATtc      <  1:1522271/69‑1 (MQ=255)
                                                       gCACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATtc      <  1:312665/69‑1 (MQ=255)
                                                       gCACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATtc      <  1:2737246/69‑1 (MQ=255)
                                                       gCACCAACGGCGCCACCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATtc      <  1:1554951/69‑1 (MQ=255)
                                                        cACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATtct     >  1:2828643/1‑69 (MQ=255)
                                                        cACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATtc      <  1:2646720/68‑1 (MQ=255)
                                                            aaCGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATAcagtc                         >  1:2335086/1‑45 (MQ=255)
                                                            aaCGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATAcagtc                         >  1:481066/1‑45 (MQ=255)
                                                            aaCGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATAcagtc                         >  1:3197136/1‑45 (MQ=255)
                                                            aaCGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATAcagtc                         >  1:968688/1‑45 (MQ=255)
                                                            aaCGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATTCTCtt  >  1:2485462/1‑68 (MQ=255)
                                                                 |                                                              
TGCTGCGCAGTGACGCAAACTTTAGCCTCAAAAAAAGGATCTTTTGCCAACGCATGCACCAACGGCGCCATCTTGATGGCTTCCGGGCGCGTACCAAATACAGTCAGTACTTTCACATCGATTCTCTT  >  minE/2428365‑2428492

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