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	252	48.5	1661298	98.8%	1641362	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,875,056	(C)_6→7	coding (521/822 nt)	nimR ←	DNA‑binding transcriptional repressor NimR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,875,050	1	.	C	94.4%	116.7 / ‑0.2	36	coding (527/822 nt)	nimR	DNA‑binding transcriptional repressor NimR
Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (13/21); total (13/23)
Fisher's exact test for biased strand distribution p-value = 5.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTTTCACTAATCCCTGAAGCGCCATAATCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATG‑CCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGAC  >  NC_000913/1874912‑1875168

ccTTTCACTAATCCCTGAAGCGCCATAATCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATG‑c                                                                                                                       >  2:5547/1‑140 (MQ=255)

  tttCACTAATCCCTGAAGCGCCATAATCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATG‑ccc                                                                                                                     <  1:519213/140‑1 (MQ=255)

          aTCCCTGAAGCGCCATAATCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATG‑cccccccactc                                                                                                             >  2:513891/1‑135 (MQ=255)

           tCCCTGAAGCGCCATAATCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCg                                                                                                             >  1:681298/1‑140 (MQ=255)

             ccTGAAGCGCCATAATCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATG‑ccccccca                                                                                                                >  2:736347/1‑132 (MQ=255)

             ccTGAAGCGCCATAATCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATG‑ccccccca                                                                                                                <  1:736347/134‑3 (MQ=255)

                    cgcCATAATCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCt                                                                                                    >  2:763464/1‑140 (MQ=255)

                          aaTCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGcc                                                                                              <  2:579383/140‑1 (MQ=255)

                           aTCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCca                                                                                             <  1:763464/140‑1 (MQ=255)

                             cAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCcatc                                                                                           <  1:210099/140‑1 (MQ=255)

                             cAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCcatc                                                                                           <  2:197440/140‑1 (MQ=255)

                             cAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCcatc                                                                                           <  2:681298/140‑1 (MQ=255)

                             cAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCcatc                                                                                           <  1:472156/140‑1 (MQ=255)

                                cTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCatcatc                                                                                        >  1:120521/1‑140 (MQ=255)

                                 tGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCTAGCCCAGTGCCCCAATGCCCCCCCACTCGACACGCCCTCTCGCCATCAtct                                                                                       >  1:52719/1‑140 (MQ=255)

                                  gTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCAtctc                                                                                      <  1:312326/140‑1 (MQ=255)

                                   tAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCACCGCAAAAAAGCCAGCCCATTGCCCCAATG‑CCCCCCACTCGACAGGCCCTTTCGCCATCATCTcca                                                                                    <  2:382739/140‑1 (MQ=255)

                                     aCTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCca                                                                                             >  1:249998/1‑130 (MQ=255)

                                     aCTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCca                                                                                             <  2:249998/130‑1 (MQ=255)

                                     aCTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTG‑CCCAATGCCCCCCCACTCGACAGGCCCTTTCg                                                                                                >  1:608792/1‑126 (MQ=255)

                                     aCTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTG‑CCCAATGCCCCCCCACTCGACAGGCCCTTTCg                                                                                                <  2:608792/126‑1 (MQ=255)

                                       tgctgACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTccacca                                                                                 <  1:5547/140‑1 (MQ=255)

                                         ctgACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTccacca                                                                                 >  1:300604/1‑138 (MQ=255)

                                         ctgACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTccacca                                                                                 <  2:300604/138‑1 (MQ=255)

                                          tgACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCcatcat                                                                                         >  1:225985/1‑129 (MQ=255)

                                          tgACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCcatcat                                                                                         <  2:225985/129‑1 (MQ=255)

                                          tgACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCg                                                                              >  2:449069/1‑140 (MQ=255)

                                            aCGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTg                                                                            <  1:449069/140‑1 (MQ=255)

                                             cGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGc                                                                           >  2:92073/1‑140 (MQ=255)

                                                    ggCGAAAGCTCATCCCCGTCTCTTTTACTATCACTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGTCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGAtttt                                                                    <  2:721224/140‑1 (MQ=255)

                                                      cGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAg                                                                  >  2:754005/1‑140 (MQ=255)

                                                               aaCCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGagaag                                                         <  2:1079/140‑1 (MQ=255)

                                                                    cGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACg                                                    >  1:378927/1‑140 (MQ=255)

                                                                          ttttACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAgg                                              <  1:289620/140‑1 (MQ=255)

                                                                           tttACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGt                                             <  2:205571/140‑1 (MQ=255)

                                                                               cTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAg                                         <  1:92073/140‑1 (MQ=255)

                                                                                    aGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACCGGCAGGTGc                                           <  2:380725/133‑1 (MQ=255)

                                                                                    aGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACCGGCAGGTGc                                           >  1:380725/1‑133 (MQ=255)

                                                                                                ttGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGgctgct                        >  1:24797/1‑140 (MQ=255)

                                                                                                    gTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAgg                    <  2:266885/140‑1 (MQ=255)

                                                                                                    gTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAgg                    <  1:754005/140‑1 (MQ=255)

                                                                                                     ttCACCCATCCCAAAAAAGCCAGCCCATTGCCCCAATG‑CCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGa                  <  2:704785/140‑1 (MQ=255)

                                                                                                                      agccagccCATTGCCCCAATGCCCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGAc  <  1:320172/140‑1 (MQ=255)

CCTTTCACTAATCCCTGAAGCGCCATAATCAGCTGTAACTGCTGACGCCACTGGCGAAAACTCAACCCCGTCTCTTTTACTATCAGTCGGGCAAGATTGCGTTCACTCATCGCAAAAAAGCCAGCCCATTGCCCCAATG‑CCCCCCACTCGACAGGCCCTTTCGCCATCATCTCCACCATCGTGCGGATTTTAGGATGAGAAGAAACGGGCAGGTGCAGCTGTTGTTGTGGCTGCTGAGGGAGTTCATCAAACAGGAC  >  NC_000913/1874912‑1875168

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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