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
A11 F50 I0 R1	804	34.5	1706502	92.5%	1578514	135.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,229,249:1	+C	17.0%	intergenic (‑143/+33)	PP_4606 ← / ← PP_4607	ferric siderophore receptor/transmembrane sensor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,229,249	1	.	C	17.0%	142.8 / 30.0	47	intergenic (‑143/+33)	PP_4606/PP_4607	ferric siderophore receptor/transmembrane sensor
Reads supporting (aligned to +/- strand): ref base . (21/18); new base C (4/4); total (25/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.81e-01

CTTCATGGACGCAGACCTGTGAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGCCACCGGGAAGCTGCCGCTGACCTTG  >  NC_002947/5229101‑5229396

cTTCATGGACGCAGACCTGTGAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACgtg‑g                                                                                                                                                    <  1:849920/150‑1 (MQ=255)

          gCAGACCTGTGAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCC‑CCCGTAGGGGCGGGTTTAc                                                                                                                                             >  2:362552/1‑147 (MQ=39)

          gCAGACCTGTGAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGGTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCC‑CCCGTAGGGGCGGGTTTAc                                                                                                                                             <  1:362552/147‑1 (MQ=39)

           cAGACCTGTGAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGt                                                                                                                                         <  2:850385/150‑1 (MQ=255)

           cAGACCTGTGAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGt                                                                                                                                         <  2:291179/150‑1 (MQ=255)

              aCCTGTGAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCACGGGTAAACCC‑CCCGTATGGGCGGGTTTACCCGCGaa                                                                                                                                      <  2:76662/150‑1 (MQ=38)

                cTGTGAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAaga                                                                                                                                    >  1:314279/1‑150 (MQ=255)

                    gAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCt                                                                                                                                <  1:568782/150‑1 (MQ=255)

                      gggggTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTgg                                                                                                                              <  2:66705/150‑1 (MQ=255)

                      gggggTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCACGGGTAAACCC‑CCCGTAGGGGCGGGTTTACCCgc                                                                                                                                         <  2:200493/139‑2 (MQ=37)

                      gggggTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCACGGGTAAACCC‑CCCGTAGGGGCGGGTTTACCCgc                                                                                                                                         >  1:200493/1‑138 (MQ=37)

                         ggTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGcac                                                                                                                           >  1:242219/1‑150 (MQ=255)

                                attGCGAATCAATCGCACTTTCACTCATTACACGGCTGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACggg‑g                                                                                                                                                    <  2:390221/118‑1 (MQ=255)

                                attGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACggg‑g                                                                                                                                                    >  1:390221/1‑118 (MQ=255)

                                       atcaatcGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGt                                                                                                                                                 <  2:716803/114‑1 (MQ=255)

                                       atcaatcGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGt                                                                                                                                                 >  1:716803/1‑114 (MQ=255)

                                            tcGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAgg                                                                                                        <  1:773586/150‑1 (MQ=255)

                                              gCACTTTCACTCATTACACGGATGTCACGTGCTGTTACCTACCATAATAGCGGAAAGATGTTTGCTGTGGCGGACTCTGCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGt                                                                                                      <  1:406072/150‑1 (MQ=255)

                                                 cTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCACGGGTAAACCC‑CCCGTAGGGGCGGGTTTACCCGCGaa                                                                                                                                      >  1:720223/1‑115 (MQ=25)

                                                 cTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCACGGGTAAACCC‑CCCGTAGGGGCGGGTTTACCCGCGaa                                                                                                                                      <  2:720223/115‑1 (MQ=25)

                                                       cTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCa                                                                                                          >  2:590886/1‑137 (MQ=255)

                                                       cTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCa                                                                                                          <  1:590886/137‑1 (MQ=255)

                                                           ttACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAac                                                                                         >  1:504124/1‑150 (MQ=255)

                                                             acacGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAacac                                                                                       >  1:202693/1‑150 (MQ=255)

                                                               acGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTAACCGTGAAGAGGATGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACgg                                                                                     >  1:57714/1‑150 (MQ=255)

                                                                            gCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAAGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGaaaa                                                                        >  1:540559/1‑150 (MQ=255)

                                                                               gTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTg                                                                                                                               >  2:96458/1‑92 (MQ=255)

                                                                               gTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGcccc                                                                                            >  1:316166/1‑127 (MQ=255)

                                                                               gTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGcccc                                                                                            <  2:316166/127‑1 (MQ=255)

                                                                               gTTACCTCACCTGTGCCGGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAGCCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTg                                                                                                                               <  1:96458/92‑1 (MQ=255)

                                                                                      taCCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAgg                                                                                                                        >  1:166228/2‑92 (MQ=255)

                                                                                      cACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAgg                                                                                                                        <  2:166228/92‑1 (MQ=255)

                                                                                       aCCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCt                                                                                                                                >  1:386834/1‑83 (MQ=255)

                                                                                       aCCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCt                                                                                                                                <  2:386834/83‑1 (MQ=255)

                                                                                                  gAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGaa                                                  >  2:772670/1‑150 (MQ=255)

                                                                                                    aaTATTTTTGCTGTGGCGGCCTCTTCGCGGGAAAAGCCGCCCCTACGGG‑GGGTTTAACCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATc                                                >  1:112370/1‑150 (MQ=255)

                                                                                                                       ccTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCg                             <  2:202693/150‑1 (MQ=255)

                                                                                                                              gcgGGGAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGCCAccc                      >  2:541376/1‑149 (MQ=255)

                                                                                                                                gggTAAACCC‑CCCGTAGGGGCGGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGCCACCggg                    >  1:504458/1‑150 (MQ=39)

                                                                                                                                 ggTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGCCACCGGGa                   >  1:591329/1‑150 (MQ=255)

                                                                                                                                  gTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGc                                                     >  2:734564/1‑115 (MQ=255)

                                                                                                                                  gTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGc                                                     <  1:734564/115‑1 (MQ=255)

                                                                                                                                  gTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGCCACCGGGaa                  >  2:111059/1‑150 (MQ=255)

                                                                                                                                   tAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGCCACCGGGAAg                 <  2:242219/150‑1 (MQ=255)

                                                                                                                                        ccGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGcc                                                                               <  1:548284/83‑1 (MQ=255)

                                                                                                                                        ccGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGcc                                                                               >  2:548284/1‑83 (MQ=255)

                                                                                                                                           ccccTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGCAACCGGGAAGCTGCCGCt         >  1:46957/1‑150 (MQ=255)

                                                                                                                                              cTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAACGAATCCAGCGCCAGCAGCGGCTCGGCCACCGGGAAGc                <  2:323886/140‑1 (MQ=255)

                                                                                                                                              cTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAACGAATCCAGCGCCAGCAGCGGCTCGGCCACCGGGAAGc                >  1:323886/1‑140 (MQ=255)

                                                                                                                                                 cGGG‑GGGTTTACCCGTGAAGAGGCTGGAACAGGCAACTATCGAACCCGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGCAACCGGGAAGCTTCCGCTGACCtt   <  2:788728/150‑1 (MQ=255)

                                                                                                                                                  ggg‑gggTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAACGGTGGTCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGGCCCCGCGAAGCTGCCGCTGACCttt  >  1:270486/1‑149 (MQ=255)

CTTCATGGACGCAGACCTGTGAGGGGGTGATTATTGCGAATCAATCGCACTTTCACTCATTACACGGATGCCACGTGCTGTTACCTCACCTGTGCCTGGAAATATTTTTGCTGTGGCGGCCTCTTCGCGGGTAAACCCGCCCCTACGGG‑GGGTTTACCCGTGAAGAGGCTGGCACAGGCAACTACCGAACCAGGGTCAAACGCCCCAACACGGTCTGCCGTGAAAAACCCATCACCTTGCCCAGCGAATCCAGCGCCAGCAGCGGCTCGGCCACCGGGAAGCTGCCGCTGACCTTG  >  NC_002947/5229101‑5229396

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A