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
A7 F28 I1 R1	172	67.8	2301510	98.9%	2276193	138.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,376,330	T→C	E149E (GAA→GAG)	sspB ←	ClpXP protease specificity‑enhancing factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,376,330	0	T	C	98.1%	172.8 / NA	52	E149E (GAA→GAG)	sspB	ClpXP protease specificity‑enhancing factor
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (28/23); total (28/24)
Fisher's exact test for biased strand distribution p-value = 4.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCGTGGTGAATATGATTGCCACAATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGTTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCTGGTATCTTCATCGTAGGCAGCTT  >  NC_000913/3376195‑3376457

ttCGTGGTGAATATGATTGCCACAATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCAt                                                                                                                             >  1:439003/1‑140 (MQ=255)

       tgAATATGATTGCCACAATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAgg                                                                                                                      <  2:608459/140‑1 (MQ=255)

          atatGATTGCCACAATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATg                                                                                                                   <  2:236527/140‑1 (MQ=255)

           tatGATTGCCACAATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGa                                                                                                                  >  2:1100901/1‑140 (MQ=255)

            atGATTGCCACAATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAg                                                                                                                 <  2:439003/140‑1 (MQ=255)

             tGATTGCCACAATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAgt                                                                                                                <  1:896918/140‑1 (MQ=255)

                     acaATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTcatcat                                                                                                        >  2:423281/1‑140 (MQ=255)

                     acaATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTcatcat                                                                                                        >  1:222904/1‑140 (MQ=255)

                         tCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTg                                                                                                    >  2:1021651/1‑140 (MQ=255)

                            cGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAgtgt                                                                                                              >  2:747340/1‑127 (MQ=255)

                            cGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAgtgt                                                                                                              <  1:747340/127‑1 (MQ=255)

                                      ttaAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCg                                                                                       <  2:222904/140‑1 (MQ=255)

                                          gTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCAt                                                                                   <  1:1021651/140‑1 (MQ=255)

                                           tCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATc                                                                                  >  2:103741/1‑140 (MQ=255)

                                            cATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCa                                                                                 <  1:103741/140‑1 (MQ=255)

                                                 aaaaGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAAc                                                                            <  1:423281/140‑1 (MQ=255)

                                                      aCAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGcc                                                                                     <  2:110075/126‑1 (MQ=255)

                                                      aCAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGcc                                                                                     >  1:110075/1‑126 (MQ=255)

                                                               gccgccTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGttt                                                              >  2:683862/1‑140 (MQ=255)

                                                                  gccTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGt                                                           >  1:508512/1‑140 (MQ=255)

                                                                   ccTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGtt                                                          >  1:381393/1‑140 (MQ=255)

                                                                    ccgggCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCg                                                            <  1:1123936/135‑1 (MQ=255)

                                                                    ccgggCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCg                                                            >  2:1123936/3‑137 (MQ=255)

                                                                    cTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTg                                                         >  1:354882/1‑140 (MQ=255)

                                                                         ccTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGc                                                    >  1:983491/1‑140 (MQ=255)

                                                                             ttttGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGAt                                                <  2:381393/140‑1 (MQ=255)

                                                                             ttttGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGAt                                                <  2:242980/140‑1 (MQ=255)

                                                                             ttttGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGAt                                                >  1:242980/1‑140 (MQ=255)

                                                                                          cacaACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGc                                              >  1:61731/1‑129 (MQ=255)

                                                                                          cacaACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGc                                              <  2:61731/129‑1 (MQ=255)

                                                                                          cacaACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTcatcat                                   >  1:539670/1‑140 (MQ=255)

                                                                                            caACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCctc                                           <  2:802361/130‑1 (MQ=255)

                                                                                            caACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCctc                                           >  1:802361/1‑130 (MQ=255)

                                                                                             aaCGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCAtcattca                                <  2:1098988/140‑1 (MQ=255)

                                                                                                 cgTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCatgat                            >  2:266547/1‑140 (MQ=255)

                                                                                                 cgTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATAATTCatgat                            >  1:104350/1‑140 (MQ=255)

                                                                                                  gTAATGCCGGTCGACCCCCGCGTGGTGGCTGCGGAGGTTCATCGTCAGGATGAGTGTAATCATCGTGATCTGGCTTGTCGCCATCACTAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCGTCATCATTCatgatg                           <  2:647431/140‑1 (MQ=255)

                                                                                                  gTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTtca                                       >  2:1135471/1‑128 (MQ=255)

                                                                                                  gTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTtca                                       <  1:1135471/128‑1 (MQ=255)

                                                                                                  gTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCatgatg                           >  1:38054/1‑140 (MQ=255)

                                                                                                  gTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATAATTCatgatg                           <  2:104350/140‑1 (MQ=255)

                                                                                                  gTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGACTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTtca                                       <  1:51984/128‑1 (MQ=255)

                                                                                                  gTAATGCCGGTCGACCACCGCGTGGGGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGACTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTtca                                       >  2:51984/1‑128 (MQ=255)

                                                                                                    aaTGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCt                         >  2:284204/1‑140 (MQ=255)

                                                                                                     aTGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGAAGCTg                        >  1:985262/1‑140 (MQ=255)

                                                                                                      tGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCTgg                       <  1:284204/140‑1 (MQ=255)

                                                                                                       gCCGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCTGGt                      <  2:25689/140‑1 (MQ=255)

                                                                                                        ccGGTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCTGGTa                     <  1:266547/140‑1 (MQ=255)

                                                                                                           gTCGACCACCGCGTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCTGGTATCt                  >  1:79586/1‑140 (MQ=255)

                                                                                                                      cgTGGTGGCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCTGGTATCTTCATCGTAGGc       >  1:730431/1‑140 (MQ=255)

                                                                                                                          gtggCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGACTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCTGGTATCTTCATCGTAGGCAGCt   >  2:332854/1‑140 (MQ=255)

                                                                                                                           tggCTGCGGAGGCTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCTGGTATCTTCATCGTAGGCAGCtt  <  1:1100901/140‑1 (MQ=255)

TTCGTGGTGAATATGATTGCCACAATCACGCTATTTTATTAAGTCATTAAAAAGACAAAACAGGCCGCCTGGGCCTGTTTTGTATTACTTCACAACGCGTAATGCCGGTCGACCACCGCGTGGTGGCTGCGGAGGTTCATCGTCAGGATGAGTGTCATCATCGTGATCTGGCTTGTCGCCATCAATAACCGACATAACGGTTTCGTTGTCTGCCGATGCCTCTTCATCATTCATGATGCTGGTATCTTCATCGTAGGCAGCTT  >  NC_000913/3376195‑3376457

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A