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 F80 I0 R1	1148	65.4	3296958	93.8%	3092546	131.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	337,822	A→C	20.1%	intergenic (‑69/+60)	PP_0279 ← / ← PP_0280	hypothetical protein/amino acid ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	337,822	0	A	C	20.1%	70.1 / 15.9	35	intergenic (‑69/+60)	PP_0279/PP_0280	hypothetical protein/amino acid ABC transporter permease
Reads supporting (aligned to +/- strand): ref base A (15/13); new base C (4/3); total (19/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.96e-01

GCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCACC  >  NC_002947/337684‑337960

gCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTgg                                                                                                                                 <  1:1300760/150‑1 (MQ=255)

 cTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCA‑CAATTTAAGGTTGgc                                                                                                                                >  2:756721/1‑150 (MQ=255)

         ggAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACAcc                                                                                                                        >  1:1170984/1‑150 (MQ=255)

           aaCTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCtg                                                                                                                      <  1:1515589/150‑1 (MQ=255)

           aaCTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCtg                                                                                                                      <  1:756721/150‑1 (MQ=255)

                gTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGa                                                                                                                 <  1:266592/150‑1 (MQ=21)

                                   gTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGc                                                                                                       <  1:1277968/141‑1 (MQ=18)

                                   gTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGc                                                                                                       >  2:1277968/1‑141 (MQ=18)

                                      cTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCCAAGcagt                                                                                           >  1:812263/1‑150 (MQ=255)

                                                   tgtgGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCtgt                                                                                                                     <  1:627372/111‑1 (MQ=255)

                                                   tgtgGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCtgt                                                                                                                     >  2:627372/1‑111 (MQ=255)

                                                                gggcagggcaAGGATGTGTGGTGGTTTTGTGGGCCTCTTCGCGGGCGCGCCCGCTCACGCAGGTATAGCGGC‑ACATTCAAGGTTGGCGCTACACCTGTGGGGGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTggcag                                                                 <  2:812263/150‑1 (MQ=255)

                                                                    aTGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACAtt                                                                                                                                          >  1:1331383/1‑73 (MQ=255)

                                                                    aTGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACAtt                                                                                                                                          <  2:1331383/73‑1 (MQ=255)

                                                                                                            gCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGc                            <  1:421491/143‑1 (MQ=255)

                                                                                                            gCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGc                            >  2:421491/1‑143 (MQ=255)

                                                                                                              aCGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCa                   >  1:77210/1‑150 (MQ=255)

                                                                                                                   cGCTCCCACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATg              >  2:1648181/1‑150 (MQ=25)

                                                                                                                      tCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAAc           >  1:776168/1‑150 (MQ=255)

                                                                                                                        ccACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAgcgc                                            <  1:184455/115‑1 (MQ=17)

                                                                                                                        ccACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAgcgc                                            >  2:184455/1‑115 (MQ=17)

                                                                                                                        ccACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACga         >  1:1150481/1‑150 (MQ=21)

                                                                                                                         cacaGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACgag        >  2:562511/1‑150 (MQ=255)

                                                                                                                         cacaGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACgag        <  2:776168/150‑1 (MQ=255)

                                                                                                                          acaGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACgaga       >  2:1093727/1‑150 (MQ=255)

                                                                                                                           caGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGc                 >  2:1581027/1‑139 (MQ=255)

                                                                                                                           caGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGc                 <  1:1581027/139‑1 (MQ=255)

                                                                                                                            aGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCAt               >  1:231568/1‑140 (MQ=255)

                                                                                                                            aGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCAt               <  2:231568/140‑1 (MQ=255)

                                                                                                                              gTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCAc   >  1:807872/1‑150 (MQ=255)

                                                                                                                               tataGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACTCTCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCAcc  <  2:807872/150‑1 (MQ=255)

                                                                                                                                ataGCGCC‑ACATTCAAGGTTGGCGCTCCACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGcc                           <  1:902803/124‑1 (MQ=255)

                                                                                                                                ataGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGcc                           >  2:902803/1‑124 (MQ=255)

                                                                                                                                 taGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTgg                                                                    >  2:1539622/1‑82 (MQ=255)

                                                                                                                                 taGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTgg                                                                    <  1:1539622/82‑1 (MQ=255)

GCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAAGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCACC  >  NC_002947/337684‑337960

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A