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
A3 F1 I1 R1 57 49.8 2216334 94.8% 2101084 113.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,901,765 G→A G152G (GGC→GGT)  bglH ← carbohydrate‑specific outer membrane porin, cryptic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,901,7650GA98.2% 184.0 / ‑6.6 54G152G (GGC→GGT) bglHcarbohydrate‑specific outer membrane porin, cryptic
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (25/28);  minor base C (0/1);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAACCAGCCGGTAGAGTACTGCTGACCAACGTTACCATCCATCATCACAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGGCCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAA  >  NC_000913/3901629‑3901900
                                                                                                                                         |                                                                                                                                       
cAAACCAGCCGGTAGAGTACTGCTGACCAACGTTACCATCCATCATCACAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGAcc                                                                                                                                       <  2:131075/139‑1 (MQ=255)
                 tACTGCTGACCAACGTTACCATCCATCATCACAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTGTTTTTGACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGcc                                                                                                                       >  1:715148/1‑139 (MQ=255)
                      ctgACCAACGTTACCATCCATCATCACAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGAt                                                                                                                 >  2:758538/1‑139 (MQ=255)
                      ctgACCAACGTTACCATCCATCATCACAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGAt                                                                                                                 <  2:507235/139‑1 (MQ=255)
                           cAACGTTACCATCCATCATCACAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGATG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAgg                                                                                                            >  1:209869/1‑139 (MQ=255)
                               gTTACCATCCATCATCACAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGaa                                                                                                        <  2:599001/139‑1 (MQ=255)
                                        catcatCACAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGagag                                                                                               >  2:244090/1‑139 (MQ=255)
                                           catcaCACCGGCATCAGCCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCg                                                                                            <  2:500937/139‑1 (MQ=255)
                                           catcaCAACGGCTTCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCg                                                                                            <  2:377816/139‑1 (MQ=255)
                                           catcaCAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCg                                                                                            >  2:559908/1‑139 (MQ=255)
                                           catcaCAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCg                                                                                            <  1:758538/139‑1 (MQ=255)
                                              cacaACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGATG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTc                                                                                         <  2:209869/139‑1 (MQ=255)
                                                caACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTT‑CCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTcccc                                                                                      >  2:195062/1‑139 (MQ=255)
                                                 aaCGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTcccc                                                                                      >  2:689546/1‑139 (MQ=255)
                                                  aCGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTccc                                                                                       >  1:472066/1‑137 (MQ=255)
                                                  aCGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTccc                                                                                       <  2:472066/137‑1 (MQ=255)
                                                   cGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCg                                                                                            <  1:3659/131‑1 (MQ=255)
                                                   cGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCg                                                                                            >  2:3659/1‑131 (MQ=255)
                                                     gCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAAc                                                                                  <  1:244090/139‑1 (MQ=255)
                                                      cATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGcc                                                                                                                       <  1:301463/101‑1 (MQ=255)
                                                      cATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGcc                                                                                                                       >  2:301463/1‑101 (MQ=255)
                                                      cATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAAcc                                                                                 <  1:559908/139‑1 (MQ=255)
                                                          aaCCCGTTTGCCGGTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGaa                                                                             <  2:591584/139‑1 (MQ=255)
                                                           aCCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAAt                                                                                                                           <  2:773669/92‑1 (MQ=255)
                                                           aCCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAAt                                                                                                                           >  1:773669/1‑92 (MQ=255)
                                                           aCCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAAc                                                                            >  2:814456/1‑139 (MQ=255)
                                                              cGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGt                                                                         <  1:689546/139‑1 (MQ=255)
                                                                tttGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGccc                                                                                                                      <  2:547217/92‑1 (MQ=255)
                                                                tttGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGccc                                                                                                                      >  1:547217/1‑92 (MQ=255)
                                                                  tGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAAt                                                                                                                           <  2:927511/85‑1 (MQ=255)
                                                                  tGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAAt                                                                                                                           >  1:927511/1‑85 (MQ=255)
                                                                                          g‑ttTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGa                                                                                                         >  2:479298/1‑79 (MQ=255)
                                                                                          g‑ttTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGa                                                                                                         <  1:479298/79‑1 (MQ=255)
                                                                                             tttAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCAt                                           <  1:814456/139‑1 (MQ=255)
                                                                                              ttAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATc                                          >  2:789099/1‑139 (MQ=255)
                                                                                                  cTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGc                                                    >  1:644085/1‑125 (MQ=255)
                                                                                                  cTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGc                                                    <  2:644085/125‑1 (MQ=255)
                                                                                                     cAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGa                                                                              <  1:486345/96‑1 (MQ=255)
                                                                                                     cAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGa                                                                              >  2:486345/1‑96 (MQ=255)
                                                                                                      aaaTCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAAc                                                                                  >  1:370170/1‑91 (MQ=255)
                                                                                                      aaaTCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAAc                                                                                  <  2:370170/91‑1 (MQ=255)
                                                                                                        aTCAAACCAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCTTTCACAAAt                                >  1:463242/1‑139 (MQ=255)
                                                                                                               cAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCTCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCttt                                       >  2:781492/1‑125 (MQ=255)
                                                                                                               cAGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCttt                                       <  1:781492/125‑1 (MQ=255)
                                                                                                                aGCCGGAGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCTTTCACAAATTTACTGaa                        <  1:789099/139‑1 (MQ=255)
                                                                                                                      aGTATTCGTTACCAAAGCGCCCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCTTTCACAAATTTACTGAAATCttt                  <  2:1063530/139‑1 (MQ=255)
                                                                                                                      aGTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCTTTCACAAATTTACTGAAATCttt                  <  2:814581/139‑1 (MQ=255)
                                                                                                                       gTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTg                                                                                                          >  1:254488/1‑50 (MQ=255)
                                                                                                                       gTATTCGTTACCAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTg                                                                                                          <  2:254488/50‑1 (MQ=255)
                                                                                                                                  cAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCg                                                                                            <  1:274982/53‑1 (MQ=255)
                                                                                                                                  cAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCg                                                                                            >  2:274982/1‑53 (MQ=255)
                                                                                                                                  cAAAGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGga      >  1:622135/1‑139 (MQ=255)
                                                                                                                                    aaGCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCTTTCACAACTTTACTGAAATCTTTCAGAGTCATGgaag    >  2:899912/1‑139 (MQ=255)
                                                                                                                                      gCGACCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGgaagaa  <  1:899912/139‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                       
CAAACCAGCCGGTAGAGTACTGCTGACCAACGTTACCATCCATCATCACAACGGCATCAACCCGTTTGCCGTTTTCGTTGTAGACACGTTG‑TTTTAACTGCAAATCAAACCAGCCGGAGTATTCGTTACCAAAGCGGCCCAGAGAACCAATCGCCCATGATTTAGGTGAACCATGAGAGGCGGTCCCCCAACCAGAACGGTAATAGCCGTTGTAACTAAAGCCAATTTCATCTTTCACAAATTTACTGAAATCTTTCAGAGTCATGGAAGAA  >  NC_000913/3901629‑3901900

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A