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
A17 F107 I0 R1 1271 54.2 2599312 94.9% 2466747 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 6,143,635 G→A 100% P72P (CCG→CCA)  cusF → copper efflux protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029476,143,6350GA98.0% 156.1 / ‑4.8 49P72P (CCG→CCA) cusFcopper efflux protein
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (19/29);  total (20/29)
Fisher's exact test for biased strand distribution p-value = 4.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.18e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGGCCGGGATGAGCATGGATGGAATGGATATGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCT  >  NC_002947/6143490‑6143777
                                                                                                                                                 |                                                                                                                                              
tGGCCGGGATGAGCATGGATGGAATGGATATGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATggccagcc                                                                                                                                             <  2:170669/149‑1 (MQ=255)
     gggATGAGCATGGATGGAATGGATATGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGAc                                                                                                                                        <  4:180321/149‑1 (MQ=255)
       gATGAGCATGGATGGAATGGATATGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCa                                                                                                                                      >  6:48968/1‑149 (MQ=255)
            gCATGGATGGAATGGATATGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGTTAAATGCAATTGACGACCAAGGCGGCACAGTGACCCTGATGCATGGACAGGTTGCTGCGTTGAAATGGCCAGCCATGACCATggac                                                                                                                                 >  5:234173/1‑147 (MQ=255)
               tggatggaATGGATATGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGGTCATGGctggc                                                                                                                              <  8:20931/149‑5 (MQ=255)
               tggatggaATGGATATGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTc                                                                                                                              <  7:270032/149‑1 (MQ=255)
                     gaatggaTATGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGACAGCCATGACCATGGCCTTCAAAGc                                                                                                                         <  6:238758/148‑1 (MQ=255)
                            tatGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTgcgc                                                                                                                 <  2:319888/149‑1 (MQ=255)
                             atGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATggccagc                                                                                                                                              <  6:255846/119‑1 (MQ=255)
                             atGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATggccagc                                                                                                                                              >  5:255846/1‑119 (MQ=255)
                               gAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCTGCAGAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGGCAGCCAGGACCagg                                                                                                                                    >  8:285756/1‑125 (MQ=255)
                               gAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCAGAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATg                                                                                                                                    <  7:285756/127‑1 (MQ=255)
                               gAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCaa                                                                                                               >  3:70151/1‑148 (MQ=255)
                                aaGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAAc                                                                                                              <  7:14086/148‑1 (MQ=255)
                                aaGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACa                                                                                                             <  1:109607/149‑1 (MQ=255)
                                  ggAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGc                                                                                                           <  8:28297/149‑1 (MQ=255)
                                  ggAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCAGCGTTGAAATGGCCAGCCATGACCATGGACGTCAAAGCCTCTGCGCAACAGc                                                                                                           >  4:4435/1‑149 (MQ=255)
                                   gAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCt                                                                                                          <  4:70151/149‑1 (MQ=255)
                                   gAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCt                                                                                                          >  5:331496/1‑149 (MQ=255)
                                       cccAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGAt                                                                                                      <  2:169178/149‑1 (MQ=255)
                                       cccAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGAt                                                                                                      <  2:174485/149‑1 (MQ=255)
                                        ccAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATg                                                                                                     >  2:100371/1‑149 (MQ=255)
                                              aGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTg                                                                                                <  5:48968/148‑1 (MQ=255)
                                                            aTGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAAc                                                                                 <  1:100371/149‑1 (MQ=255)
                                                              gCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACg                                                                                >  4:108350/1‑148 (MQ=255)
                                                                 gAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTaga                                                                            <  7:81524/149‑1 (MQ=255)
                                                                    gggACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTc                                                                                                                              <  1:36591/96‑1 (MQ=255)
                                                                    gggACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTc                                                                                                                              >  2:36591/1‑96 (MQ=255)
                                                                     ggACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGATCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGttt                                                                        <  4:144775/149‑1 (MQ=255)
                                                                     ggACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGttt                                                                        <  8:209199/149‑1 (MQ=255)
                                                                     ggACGGTAAAGGCAATTGACCCCCAAGGCGGCCAAGTGACCCTCATGCATGGACCGTTTGCTGCGTTTAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGAAACAGCTCGATGGATTTAAGGTGGTAGACAACGTATAGttg                                                                        <  6:234173/149‑2 (MQ=255)
                                                                          gTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCAt                                                                                                                                           <  8:143585/77‑1 (MQ=255)
                                                                          gTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCAt                                                                                                                                           >  7:143585/1‑77 (MQ=255)
                                                                              aGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCAAGGCCATCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTcgg                                                                >  7:210113/1‑146 (MQ=255)
                                                                                  aaTTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCggatg                                                            >  1:263292/1‑148 (MQ=255)
                                                                                   aTTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCggatgga                                                          >  6:269331/1‑149 (MQ=255)
                                                                                        cGCCGATGGCGGCACAGTGATCCTGATGCATGGACCGGTTGCGGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACTTAGAGTTTGATTTCCGGATGGATGgc                                                      <  8:210113/148‑1 (MQ=255)
                                                                                         gCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCAAGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGgcag                                                    >  5:139810/1‑149 (MQ=255)
                                                                                          cccAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGgcagc                                                   <  2:263292/149‑1 (MQ=255)
                                                                                                   gcACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGAt                                                                                                  >  6:17366/1‑93 (MQ=255)
                                                                                                   gcACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGAt                                                                                                  <  5:17366/93‑1 (MQ=255)
                                                                                                     acaGTGACCCTGATGCATGGACCGGTTGCTTCGTTGAAATGGCCATCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGAt                                        <  4:26296/149‑1 (MQ=255)
                                                                                                      caGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGAtt                                       <  3:77536/149‑1 (MQ=255)
                                                                                                             ccTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGata                                >  7:114671/1‑149 (MQ=255)
                                                                                                             ccTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGata                                >  5:320455/1‑149 (MQ=255)
                                                                                                                gATGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTc                             >  3:150057/1‑149 (MQ=255)
                                                                                                                 aTGCATGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATAtt                              <  6:331496/147‑1 (MQ=255)
                                                                                                                     aTGGACCGGTTGCTGCGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCaaa                        >  8:188429/1‑149 (MQ=255)
                                                                                                                                  tgcGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGcc            >  6:188635/1‑148 (MQ=255)
                                                                                                                                    cGTTGAAATGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTaa         <  4:37378/149‑1 (MQ=255)
                                                                                                                                         aaaTGGCCAGCCATGACCAAGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTTGCCTAATTATc    <  6:139810/149‑1 (MQ=255)
                                                                                                                                           aTGGCCAGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCt  <  6:320455/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                              
TGGCCGGGATGAGCATGGATGGAATGGATATGAAGGAAACCCAATCAGCACCTTCCGCTCATGCAGAAGGGACGGTAAAGGCAATTGACGCCCAAGGCGGCACAGTGACCCTGATGCATGGACCGGTTGCTGCGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCT  >  NC_002947/6143490‑6143777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ 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