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 F1 I1 R1 81 47.9 2225048 94.8% 2109345 113.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 585,317 C→T W106* (TGG→TAG)  ompT ← DLP12 prophage, outer membrane protease VII, outer membrane protein 3b

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913585,3170CT100.0% 186.9 / NA 53W106* (TGG→TAG) ompTDLP12 prophage, outer membrane protease VII, outer membrane protein 3b
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/27);  total (26/27)

CAGGCGGTAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCACCTTTAATAATTGCAGCGTTATTGAATT  >  NC_000913/585190‑585440
                                                                                                                               |                                                                                                                           
cAGGCGGTAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCg                                                                                                                  <  1:363765/139‑1 (MQ=255)
    cGGTAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCa                                                                                                              <  2:846741/139‑1 (MQ=255)
       tAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTcc                                                                                                                        >  1:1035215/1‑126 (MQ=255)
       tAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTcc                                                                                                                        <  2:1035215/126‑1 (MQ=255)
             ggTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCAc                                                                                                     >  1:1076237/1‑139 (MQ=255)
                  gTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCgg                                                                                                <  2:993090/139‑1 (MQ=255)
                           ccagccTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCgaga                                                                                       <  1:854673/139‑1 (MQ=255)
                             agccTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGt                                                                                     >  1:655317/1‑139 (MQ=255)
                                         tCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCcagccagc                                                                         >  1:59173/1‑139 (MQ=255)
                                         tCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCcagccagc                                                                         >  2:478026/1‑139 (MQ=255)
                                         tCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCcagccagc                                                                         >  2:1105844/1‑139 (MQ=255)
                                             aTCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAg                                                                                                                           <  1:19904/85‑1 (MQ=255)
                                             aTCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGATTCCGGGGTTACTGGAATCCATCTAg                                                                                                                           >  2:19904/1‑85 (MQ=255)
                                              tCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGccc                                                                    <  1:517387/139‑1 (MQ=255)
                                                  aTTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCt                                                                                                   >  2:68984/1‑104 (MQ=255)
                                                  aTTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCt                                                                                                   <  1:68984/104‑1 (MQ=255)
                                                  aTTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCgat                                                                <  1:386635/139‑1 (MQ=255)
                                                  aTTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCgat                                                                >  2:630660/1‑139 (MQ=255)
                                                  aTTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCgat                                                                >  1:755507/1‑139 (MQ=255)
                                                   ttCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCgata                                                               <  2:794463/139‑1 (MQ=255)
                                                              aaTTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTgggg                                                    <  1:630660/139‑1 (MQ=255)
                                                                     ttGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCaaa                                             <  2:548321/139‑1 (MQ=255)
                                                                          tATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCa                                        >  1:513063/1‑139 (MQ=255)
                                                                             cAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCcagccagc                                                                         <  1:496762/103‑1 (MQ=255)
                                                                             cAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCcagccagc                                                                         >  2:496762/1‑103 (MQ=255)
                                                                                  tgtCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTg                                >  1:446270/1‑139 (MQ=255)
                                                                                  tgtCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTg                                >  1:137896/1‑139 (MQ=255)
                                                                                    tCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGccc                                                                    <  2:393601/101‑1 (MQ=255)
                                                                                    tCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGccc                                                                    >  1:393601/1‑101 (MQ=255)
                                                                                    tCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCa                              >  1:452841/1‑139 (MQ=255)
                                                                                    tCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCa                              <  2:59173/139‑1 (MQ=255)
                                                                                    tCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCa                              <  1:1105844/139‑1 (MQ=255)
                                                                                    tCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCa                              <  2:1076237/139‑1 (MQ=255)
                                                                                    tCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCa                              >  1:1037261/1‑139 (MQ=255)
                                                                                      tACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCcagcag                                                                       <  2:356114/96‑1 (MQ=255)
                                                                                      tACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCcagcag                                                                       >  1:356114/1‑96 (MQ=255)
                                                                                      tACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCAcc                            >  2:183835/1‑139 (MQ=255)
                                                                                         tttCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGAc                                                                                                                >  2:454657/1‑52 (MQ=255)
                                                                                         tttCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGAc                                                                                                                <  1:454657/52‑1 (MQ=255)
                                                                                              tCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGccc                                                                    <  2:987665/91‑1 (MQ=255)
                                                                                              tCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGccc                                                                    >  1:987665/1‑91 (MQ=255)
                                                                                              tCCGTCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCACCTTtaataa                    >  1:926821/1‑139 (MQ=255)
                                                                                                  tCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATc                                           >  2:258499/1‑112 (MQ=255)
                                                                                                  tCCAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATc                                           <  1:258499/112‑1 (MQ=255)
                                                                                                   ccAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCACCTTTAATAATTGCa               <  2:22263/139‑1 (MQ=255)
                                                                                                   ccAGGTTCCGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCACCTTTAATAATTGCa               <  2:513063/139‑1 (MQ=255)
                                                                                                           cGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCgat                                                                >  2:192961/1‑82 (MQ=255)
                                                                                                           cGGGGTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCgat                                                                <  1:192961/82‑1 (MQ=255)
                                                                                                            ggggTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTggg                                                     <  2:716372/92‑1 (MQ=255)
                                                                                                            ggggTTACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTCTCCAGCCAGCAGCCCCGATAGATATCTggg                                                     >  1:716372/1‑92 (MQ=255)
                                                                                                                ttACTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCACCTTTAATAATTGCAGCGTTATTGAAtt  <  2:1037261/139‑1 (MQ=255)
                                                                                                                   cTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCa                                        >  2:1001868/1‑98 (MQ=255)
                                                                                                                   cTGGAATCCATCTAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCa                                        <  1:1001868/98‑1 (MQ=255)
                                                                                                                        atccatctAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGccc                                                                    <  2:1005358/65‑1 (MQ=255)
                                                                                                                        atccatctAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGccc                                                                    >  1:1005358/1‑65 (MQ=255)
                                                                                                                            atctaGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGccc                                                                    >  1:1085901/1‑61 (MQ=255)
                                                                                                                               |                                                                                                                           
CAGGCGGTAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGATCGACCATATTGCCACCTCGGCTGCCGAGAGTTGTCCAGCCAGCAGCCCCGATAGATATCTGGGGCATCAAATCCCAATTAATTGCACCTTTAATAATTGCAGCGTTATTGAATT  >  NC_000913/585190‑585440

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A