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
A12 F28 I1 R1	227	52.0	1764248	99.3%	1751898	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,601,601	(G)_5→6	coding (112/1536 nt)	lsrA →	Autoinducer‑2 ABC transporter ATP binding subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,601,596	1	.	G	91.5%	149.7 / 7.3	47	coding (107/1536 nt)	lsrA	Autoinducer‑2 ABC transporter ATP binding subunit
Reads supporting (aligned to +/- strand): ref base . (2/2); new base G (21/22); total (23/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.39e-01

TGCAAAACTGAACGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCA‑G‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGTCAGATTAACGCCAG  >  NC_000913/1601468‑1601730

tGCAAAACTGAACGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTc                                                                                                                              <  1:420573/140‑1 (MQ=255)

  cAAAACTGAACGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCa                                                                                                                            >  1:147381/1‑140 (MQ=255)

  cAAAACTGAACGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCa                                                                                                                            >  1:384704/1‑140 (MQ=255)

  cAAAACTGAACGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCa                                                                                                                            >  1:351780/1‑140 (MQ=255)

  cAAAACTGAACGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCa                                                                                                                            >  1:277469/1‑140 (MQ=255)

  cAAAACTGAACGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCa                                                                                                                            >  1:236148/1‑140 (MQ=255)

         gAACGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTg                                                                                                                     <  1:498492/140‑1 (MQ=255)

            cGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTc                                                                                                                  <  1:819537/140‑1 (MQ=255)

               gggAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTcggc                                                                                                               >  2:562534/1‑140 (MQ=255)

                     tatGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAAt                                                                                                         <  1:328732/140‑1 (MQ=255)

                          aaaCGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGc                                                                                                    <  1:415075/140‑1 (MQ=255)

                               aGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTa                                                                                               >  1:57702/1‑140 (MQ=255)

                                          cgcgTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTa                                                                                    >  1:154513/1‑140 (MQ=255)

                                          cgcgTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTa                                                                                    >  1:815651/1‑140 (MQ=255)

                                          cgcgTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTa                                                                                    >  2:644633/1‑140 (MQ=255)

                                              ttACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGa                                                                                <  2:129581/140‑1 (MQ=255)

                                                        tttGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGc                                                                      <  2:154513/140‑1 (MQ=255)

                                                        tttGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGc                                                                      <  1:547236/140‑1 (MQ=255)

                                                         ttGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGcc                                                                     <  1:562534/140‑1 (MQ=255)

                                                              cccGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTAt                                                                <  2:147381/140‑1 (MQ=255)

                                                                     ggTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCct                                                         <  1:697275/140‑1 (MQ=255)

                                                                     ggTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCct                                                         <  2:815651/140‑1 (MQ=255)

                                                                                 gTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGt                                             <  2:99779/140‑1 (MQ=255)

                                                                                 gTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGt                                             >  1:506436/1‑140 (MQ=255)

                                                                                   aTTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTAc                                           <  2:403849/140‑1 (MQ=255)

                                                                                    ttCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACg                                          >  2:262567/1‑140 (MQ=255)

                                                                                    ttCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCA‑G‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGc                                         >  1:296014/1‑140 (MQ=255)

                                                                                    ttCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCA‑G‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGc                                         >  1:811634/1‑140 (MQ=255)

                                                                                          ggTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGCGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGCACGCTGgac                                    >  2:577866/1‑139 (MQ=255)

                                                                                          ggTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGgag                                    >  1:766172/1‑140 (MQ=255)

                                                                                            tCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGAt                                  >  1:102745/1‑140 (MQ=255)

                                                                                            tCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGAt                                  >  1:486885/1‑140 (MQ=255)

                                                                                            ccAATGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGAt                                  >  2:6557/2‑140 (MQ=255)

                                                                                              aaTGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTg                                <  1:644633/140‑1 (MQ=255)

                                                                                               aTGTCCTG‑AAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAg                              <  1:774279/140‑1 (MQ=255)

                                                                                                tGTCCTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAg                              <  1:673022/140‑1 (MQ=255)

                                                                                                   ccTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGt                                             <  1:67205/122‑1 (MQ=255)

                                                                                                   ccTGAAAGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGt                                             >  2:67205/1‑122 (MQ=255)

                                                                                                       gaaGGCATCGATTTTACGTTGCATCA‑GCGGGGAGGACCACGCCCTGCTCGAAGGCAATGGTGCAGGTAAATCGACGTTAATGAAGACTATTGCCGGTATTACGCCTGCTGATAGCGGTACGCTGCAGATTGAGGGcaaga                       >  2:774279/2‑138 (MQ=255)

                                                                                                       aaaGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGcaaca                       >  1:658602/1‑140 (MQ=255)

                                                                                                       aaaGGCATCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGcaaca                       >  1:288752/1‑140 (MQ=255)

                                                                                                              tCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGt                >  2:404381/1‑140 (MQ=255)

                                                                                                              tCGATTTTACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGt                <  2:351780/140‑1 (MQ=255)

                                                                                                                   tttACGTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGTCAGAt           <  1:76838/140‑1 (MQ=255)

                                                                                                                       cGTTGCATCA‑G‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGTCAGATTAACg      <  2:296014/140‑1 (MQ=255)

                                                                                                                       cGTTGCATCA‑G‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGTCAGATTAACg      <  2:811634/140‑1 (MQ=255)

                                                                                                                        gTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGTCAGATTAACg      <  2:277469/140‑1 (MQ=255)

                                                                                                                        gTTGCATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGTCAGATTAACg      <  2:236148/140‑1 (MQ=255)

                                                                                                                            cATCAGG‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGTCAGATTAACGCCAg  >  1:522137/1‑140 (MQ=255)

TGCAAAACTGAACGGGGGAAATATGCAAACGAGTGATACCCGCGCGTTACCGCTACTTTGCGCCCGCTCGGTTTATAAACAGTATTCAGGGGTCAATGTCCTGAAAGGCATCGATTTTACGTTGCATCA‑G‑GGGGAGGTCCACGCCCTGCTCGGCGGCAATGGTGCCGGTAAATCGACGTTAATGAAGATTATTGCCGGTATTACCCCTGCTGATAGCGGTACGCTGGAGATTGAGGGCAACAACTACGTCAGATTAACGCCAG  >  NC_000913/1601468‑1601730

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