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 F14 I0 R1 206 76.7 3255580 98.8% 3216513 146.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 6,135,378 A→T 24.3% H430Q (CAT→CAA)  copA‑II ← copper resistance protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC6,135,3780AT24.3% 81.5 / 8.8 56H430Q (CAT→CAA) copA‑IIcopper resistance protein A
Reads supporting (aligned to +/- strand):  ref base A (18/21);  new base T (3/11);  total (22/34)
Fisher's exact test for biased strand distribution p-value = 1.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCATGTTGCCGTGG  >  NC_002947_CJ‑RC/6135236‑6135525
                                                                                                                                              |                                                                                                                                                   
gttcgaTCCGAGCCATATTGGTATGGTCGATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGt                                                                                                                                                 <  3:145599/142‑1 (MQ=18)
    cATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATcc                                                                                                                                           <  2:236270/149‑1 (MQ=255)
       cccAGCCATCTTGCTATTGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATccc                                                                                                                                          <  7:360069/147‑1 (MQ=255)
          aGCCATCTTGCTATGGTCCATATCGGCCATACCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGACGCCGTGGTCCATCACAGCCATTTTGCTGTGGTCCATGCCGGACATGCTGCCTTGGTCCATCCCAGCCa                                                                                                                                     >  1:153414/1‑149 (MQ=17)
            ccATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCAtt                                                                                                                                   >  4:200586/1‑149 (MQ=255)
            ccATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCAGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCAt                                                                                                                                    >  5:188775/1‑148 (MQ=255)
             cATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGTCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCAttt                                                                                                                                  <  4:45867/149‑1 (MQ=255)
              aTCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCAttt                                                                                                                                  <  8:279637/148‑1 (MQ=255)
                   gCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGc                                                                                                                               <  4:201114/146‑1 (MQ=255)
                   gCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCAGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGACATGGTCCATCCCAGCCATTTTGCtgt                                                                                                                            >  4:375521/1‑149 (MQ=255)
                   gCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGACATGATGCCGTGGTCCATCAAAGCCATTTTGCTGTGATCCATGCAGAACATGATACCATGGTCCATGCAAACAAtttttaagt                                                                                                                            >  2:397457/1‑144 (MQ=17)
                          tCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCGGCCGTGGTCCATCGCAGCCATTTTGCTGTGGTCCATGCCGGCCATGCTGCCTTGGTCCATCCCAGCAAGTTTGAAGTGGTCCAt                                                                                                                     >  1:296713/1‑149 (MQ=14)
                            cATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCTGCCGTGGTCCATCACAGCCATTTTGCTGTGATCCATGCCGGGCATGATGCATTGGTACATCCCAGGCATTTTGCAGTggggcatt                                                                                                                    >  8:159091/1‑142 (MQ=17)
                              tatCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCg                                                                                                                 <  1:303588/149‑1 (MQ=255)
                               atCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGAAGCCGTGGTCCATCACAGCCATTTTGCAGTGATCAATGCCGGGCATGATACCGTGGTCCATCCAAGCCATTTTACGGTGGTCGAtaaag                                                                                                                 >  2:262577/1‑144 (MQ=17)
                                    ccATGCCGCCTTGGTCCATCCCATCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGTTCCATCTCAGCCATTTTGCTGTGTTCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGt                                                                                                               <  4:70316/145‑1 (MQ=255)
                                      aTGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGCTCCATGCCGGCCATGCTGCCTTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGt                                                                                                          <  8:188465/148‑1 (MQ=255)
                                      aTGCCGCCTTGGTCAATCCCTGCCATCTTGCTGTGGTCGTTGTCTGCCTTGCCGGCTTGGTCCATCTCTGCCATTTTGCTTTGATCCATGTCGGCCATGATGGCATGGTGCATCCCATCCATTTTGCTGTGGTCCATGACGGTCATGtt                                                                                                         <  2:112889/149‑1 (MQ=17)
                                         ccgccTTGGTCCATAGGTTCGATCTTGCTTGGGTCCTTGTCTGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTTTGATCGATGCCTGCCATGCTGCCCTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGttt                                                                                                        <  8:313218/147‑2 (MQ=17)
                                            ccTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTg                                                                                                   <  1:211192/149‑1 (MQ=255)
                                            ccTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCAGCCGTGGTCCATCACAGCCATTTTGCTGTGATCCATGCCGGCCATGATGACATGGTCAATCCCTGCGATATTGCTGTTGTCAATGACGGTCATGTTGCGGt                                                                                                    >  8:261804/1‑148 (MQ=18)
                                             cTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCAGCCGTGGTCCATCACAGCCATTTTGCTGTGATCCATGCCGGCCATGATGACATGGTCCATCCCAGCCATATTGCGTTGGTCCAAGCCGGACATGATGCCGtc                                                                                                   >  8:14490/1‑147 (MQ=14)
                                                    cATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATc                                                                                            <  3:164523/148‑1 (MQ=255)
                                                      tCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATccc                                                                                          <  6:188775/148‑1 (MQ=255)
                                                          aGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCa                                                                                     >  1:17850/1‑149 (MQ=255)
                                                              aTCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCAATTCTGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGATGTGGTCAATGCCGGTCATGTTGCCGTGGTCAATACCAGCCAtttt                                                                                 >  2:78426/1‑149 (MQ=25)
                                                               tCTTGCTGTGGTCCATGCCGGCCATGCAGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCAATGCCGGCCATGATGACATGGTGCAACCCATCAATTTTTATGTGGTCCATGCAGGGCATGTTGGCGGGGTGCGGCCCAGCAAttt                                                                                  >  6:306735/1‑147 (MQ=18)
                                                                    cTGAGGGCCATGCCGGCCATGCCGCCGCGGTCCATCTCAGCCATATTGCCGTGGTCCATGCCGGCCATGCGGCCTTGGTCCATCCCATCCATTTTGCTGTGGTCCATGCCGGGCATGTTGCCGTGGTCCATCCCAGCCATTTTGCtgtg                                                                           <  2:344018/149‑1 (MQ=14)
                                                                     tgtgGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTgg                                                                          >  3:192208/1‑149 (MQ=255)
                                                                       tgGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCTGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGt                                                                         <  1:78426/148‑1 (MQ=255)
                                                                       tgGTCCATCGCGGACATGCAGGCTTCTTCCATCGCAGCCATTTTGCTGTGCTCCATTGCGGCCATGCTGCCTTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCtgtg                                                                           <  4:49258/146‑1 (MQ=14)
                                                                            cATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCAt                                                                                             <  5:209844/123‑1 (MQ=255)
                                                                            cATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCAt                                                                                             >  6:209844/1‑123 (MQ=255)
                                                                            cATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGc                                                                   >  4:185011/1‑149 (MQ=255)
                                                                              tgaccgCCATCCCGCCGTGTTCCATCCCAGCCATTCTGCTGTGCTCCATCCCGGCCATGCTGCCTTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGCTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGcc                                                                  <  6:320087/143‑1 (MQ=11)
                                                                                   gCCATGACGCCGTGGTCCATCTCATCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCa                                                             <  5:239742/148‑1 (MQ=255)
                                                                                        gccgccGTGGTCCATCTCAGCCATTTTGCTGTCATCCATGCCGGCCATGCGGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTg                                                        <  5:332770/148‑1 (MQ=255)
                                                                                          cgccgTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGACGGTAATGTTGCCGTGGTCCATCCAAGCCATTTTGCTGTGTTCCAAGCAGTCCAGGTTGcc                                                      >  5:125623/1‑148 (MQ=17)
                                                                                             cgTGGTCCATCTCAGCCATTTTGCTGTGCTCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTgg                                                  <  2:41248/149‑1 (MQ=255)
                                                                                              gTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATTCTGCCATGGTCCATCCCAGCCATATTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTgg                                                  <  7:261804/148‑1 (MQ=255)
                                                                                                 gTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCCGCCATTATGCAGTGGTCCATACCGCGCATGTTGCCGGGGGCCAAACCAGCCATAATGCAGTGGTCAAGACCCGCCTGGTTGCAGTgggca                                               >  2:403841/1‑145 (MQ=255)
                                                                                                    cATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGATCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATc                                            >  5:351227/1‑148 (MQ=255)
                                                                                                       ctcAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCAGTGGTCCATGCCGTCAATGTTGCAGTGGTCCaggc                                           >  3:21457/1‑143 (MQ=14)
                                                                                                        tcAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGcc                                                                                                      >  3:107509/1‑86 (MQ=255)
                                                                                                        tcAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGcc                                                                                                      <  4:107509/86‑1 (MQ=255)
                                                                                                          atccATTTTTCTGGGCTCCATCCCGGCCATCCTGCCTTGTTCCATCCCATCCATTTTGCTTTGGTCCATGGCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATTCCGGCCATGTTGCCGTGGTCCATCCCAGCCa                                     <  4:345255/147‑1 (MQ=14)
                                                                                                          aGCAATTTTGTGTTGATGCTTGCCTGCCATTCTGCCTTGGTCCATACCAGCATTTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGTTCCATGCCGGCCATGTTGCCGTGGTCCATccc                                          <  6:125623/144‑1 (MQ=14)
                                                                                                                   ccacacctCCATCCCGGCCATGCAGCCTTGGTCCATCCCAGCCACTTTGCTTTGGTCCATCCCGGCCATGGCGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCt                              <  5:19258/140‑1 (MQ=11)
                                                                                                                    ctctgctCCATCCCGGCCATGCTGCCTTGGCCCATCCCAGCCCTTTTTCTGTGGTCCATGCCGGGCATGCTGCCGTGGTCCATCCCAGCCATATTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCtgt                            <  5:407066/142‑1 (MQ=14)
                                                                                                                        tatccatccCGGCCATGCTGCCTTGTTCTATCACATCCATTTTTCTGATGTCCATCTCGGCCATGCTGCCTTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTc                        <  7:114212/147‑1 (MQ=11)
                                                                                                                        gttCCATGCCGGCCATGCTGCCTTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTc                        <  2:222481/146‑1 (MQ=255)
                                                                                                                                   gCCATGCTGCCTTTGTCCATCTCTGCGATTTTTCTGTGGTCCATGCCGGTCATGTTGCCTTGGTCCATCCCTGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCAt            <  2:212239/149‑1 (MQ=14)
                                                                                                                                   gCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCAt            <  2:17850/149‑1 (MQ=255)
                                                                                                                                    ccATGCTGCCCTGGTCCACCCCAGCCATTTTGCTGTGGTCCATGCCGGTCTTTTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCAt            <  5:306735/148‑1 (MQ=255)
                                                                                                                                         ctcccATGGTCCATCCCCCCCATTTTGCTGTTGTCCATGCCGGTCATGTTGCCTTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCATGTTGc       <  5:219474/145‑1 (MQ=14)
                                                                                                                                             cATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGACATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGAAATGTTGACGTGGTACATACCAGACATTTTTCAGTGGTCCATAAATGAAATGTTGCCgggg  >  4:308052/1‑149 (MQ=14)
                                                                                                                                              |                                                                                                                                                   
GGTCCATCCCAGCCATCTTGCTATGGTCCATATCGGCCATGCCGCCTTGGTCCATCCCAGCCATCTTGCTGTGGTCCATGCCGGCCATGCCGCCGTGGTCCATCTCAGCCATTTTGCTGTGATCCATGCCGGCCATGCTGCCATGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGTCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATGCCGGCCATGTTGCCGTGGTCCATCCCAGCCATTTTGCTGTGGTCCATACCGGCCATGTTGCCGTGG  >  NC_002947_CJ‑RC/6135236‑6135525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A