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
A5 F43 I1 R1 6 69.6 3402438 93.9% 3194889 134.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947 1,648,882 +T intergenic (‑119/+177) oprB‑II ← / ← PP_1446 carbohydrate‑selective porin/TonB‑dependent receptor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,648,8811.T97.9% 150.5 / ‑3.4 48intergenic (‑118/+178)oprB‑II/PP_1446carbohydrate‑selective porin/TonB‑dependent receptor
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base T (23/24);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

CCGATGTAGCAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGA‑TATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTATTCGCGGGT  >  NC_002947/1648732‑1649022
                                                                                                                                                       |                                                                                                                                             
ccGATGTAGCAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGgga‑gga                                                                                                                                                <  1:1548237/150‑1 (MQ=255)
 cGATGTAGCAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGa‑t                                                                                                                                              >  1:1539481/1‑150 (MQ=255)
         cAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAgggg                                                                                                                                       >  2:769090/1‑150 (MQ=255)
                 aGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTtata                                                                                                                               <  2:1316507/150‑1 (MQ=255)
                    cAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGGAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCTATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGa                                                                                                                            <  1:46070/150‑1 (MQ=255)
                      gTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGaaa                                                                                                                          <  2:1539481/150‑1 (MQ=255)
                             cATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACa                                                                                                                   >  1:1057344/1‑150 (MQ=255)
                                              ttttGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAtt                                                                                                  >  2:164379/1‑150 (MQ=255)
                                              ttttGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAtt                                                                                                  >  1:1270501/1‑150 (MQ=255)
                                                 tGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCTCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgtt                                                                                               <  1:769090/150‑1 (MQ=255)
                                                 tGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgtt                                                                                               <  1:1138812/150‑1 (MQ=255)
                                                 agataaatGAAAAAAACAGCAAACACATCGAAAGGCGGGTCCTTCAATGGATATGGCGACAAGATAGTTCGATGAAACGTTTCAACTTGCGACGGGGA‑CGATTATAGGAAAAAAAAAAAAAAAAAAGACAAATTGTCGCAGAGGAttgtt                                                                                               <  2:664602/143‑1 (MQ=255)
                                                       ttGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACaa                                                                                                                  <  2:1698132/125‑1 (MQ=255)
                                                       ttGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACaa                                                                                                                  >  1:1698132/1‑125 (MQ=255)
                                                       ttGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGAAATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGaa                                                                                         >  1:820320/1‑150 (MQ=255)
                                                        tGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGa                                                                                                                     >  1:424871/1‑121 (MQ=255)
                                                        tGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAAAAAAAAGa                                                                                                                     <  2:424871/121‑1 (MQ=255)
                                                          aaaaaaaCGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACgg                                                                                      <  1:164379/150‑1 (MQ=255)
                                                            aaaaaCGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGc                                                                                    <  2:1057344/150‑1 (MQ=255)
                                                             aaaaCGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGGGTCGGGGA‑GGATTATCGGGGAGGATCTCAGCGATAATACAGAATGTCGCAGAGGATTGTTGTTGAACGGGCa                                                                                   >  1:381421/1‑150 (MQ=255)
                                                              aaaCGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGGTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCaa                                                                                  >  1:1553557/1‑150 (MQ=255)
                                                                  ggCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAgggg                                                                                                                                       >  1:67831/1‑93 (MQ=255)
                                                                  ggCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAgggg                                                                                                                                       <  2:67831/93‑1 (MQ=255)
                                                                     aaGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAgtcgt                                                                           >  1:1467999/1‑150 (MQ=255)
                                                                               aaGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGa                                                                 >  2:860783/1‑150 (MQ=255)
                                                                               aaGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGa                                                                 <  1:1034885/150‑1 (MQ=255)
                                                                                       gcCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGgtg                                                         >  1:588746/1‑150 (MQ=255)
                                                                                           cTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATaa                                                                                                                              >  2:550534/1‑77 (MQ=255)
                                                                                           cTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATaa                                                                                                                              <  1:550534/77‑1 (MQ=255)
                                                                                           cTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAgg                                                     >  1:1424571/1‑150 (MQ=255)
                                                                                               aTGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTCCAATGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCg                                                 <  1:1037138/150‑1 (MQ=255)
                                                                                                   atatGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACaaa                                                                                                                 <  1:1399964/82‑1 (MQ=255)
                                                                                                   atatGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACaaa                                                                                                                 >  2:1399964/1‑82 (MQ=255)
                                                                                                        gCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGAGGGT‑TATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgttg                                                                                              >  1:755354/1‑96 (MQ=255)
                                                                                                        gCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgttg                                                                                              <  2:755354/96‑1 (MQ=255)
                                                                                                          gACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGTGGAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCcgc                                      >  1:185526/1‑150 (MQ=255)
                                                                                                          gACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGgt                                                          <  1:1136703/130‑1 (MQ=255)
                                                                                                          gACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGgt                                                          >  2:1136703/1‑130 (MQ=255)
                                                                                                              aGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAAt                                  <  2:1089874/150‑1 (MQ=255)
                                                                                                                aTTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATgc                                >  1:378371/1‑150 (MQ=255)
                                                                                                                       gATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgttg                                                                                              <  2:1510682/81‑1 (MQ=255)
                                                                                                                       gATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGAttgttg                                                                                              >  1:1510682/1‑81 (MQ=255)
                                                                                                                       gATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGtt                         >  2:1012128/1‑150 (MQ=255)
                                                                                                                                tttCACCTGCCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCa                >  2:848895/1‑150 (MQ=255)
                                                                                                                                 ttCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCAt               >  2:602249/1‑150 (MQ=255)
                                                                                                                                  tCAGCTTGCGGCGGGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATc              <  2:381421/150‑1 (MQ=255)
                                                                                                                                            gcggGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTCCCATCGTCTTCGCgg    <  2:1270501/150‑1 (MQ=255)
                                                                                                                                            gcggGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTATTCGCgg    <  2:879800/150‑1 (MQ=255)
                                                                                                                                            gcggGGA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTATTCGCgg    <  1:848895/150‑1 (MQ=255)
                                                                                                                                              ggggA‑GGATTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTATTCGCGGGt  <  1:479122/150‑1 (MQ=255)
                                                                                                                                                 ga‑ggatTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTa           >  1:393311/1‑138 (MQ=255)
                                                                                                                                                 ga‑ggatTATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTa           <  2:393311/138‑1 (MQ=255)
                                                                                                                                                       |                                                                                                                                             
CCGATGTAGCAGGTTTTAGGCAGTTGGAACATGAGATAGCGCTATCTTTTGATTATTGAAAAAAACGGCAAGCGCATCGAAGGGCGGGCCCCTCAATGGATATGGCGACAAGATTGTTCGATGAAGCGTTTCAGCTTGCGGCGGGGA‑GGA‑TATAGGGGAAGTTATAAGAAAAAAGACAAATTGTCGCAGAGGATTGTTGTTGAACGGGCAACAGTCGTCATTAATCGAGGCAGGTGTAGGAGCGGGTTCACCCGCGAATGCGCCGGTTGCCCTACCATCGTATTCGCGGGT  >  NC_002947/1648732‑1649022

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A