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
A2 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,644,942	C→T	intergenic (‑40/+177)	rem ← / ← hokD	Qin prophage; uncharacterized protein/Qin prophage; small toxic polypeptide

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,644,942	0	C	T	94.7%	126.2 / ‑1.3	38	intergenic (‑40/+177)	rem/hokD	Qin prophage; uncharacterized protein/Qin prophage; small toxic polypeptide
Reads supporting (aligned to +/- strand): ref base C (2/0); new base T (18/18); total (20/18)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01

CGCAAACACATAATGCGGTAATGACTAACAAGATTTCCATTTTCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAG  >  NC_000913/1644796‑1645085

cGCAAACACATAATGCGGTAATGACTAACAAGATTTCCATTTTCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGatcatc                                                                                                                                             >  2:310628/1‑151 (MQ=255)

cGCAAACACATAATGCGGTAATGACTAACAAGATTTCCATTTTCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCAt                                                                                                                                              <  1:297802/150‑1 (MQ=255)

           aaTGCGGTAATGACTAACAAGATTTCCATTTTCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATccc                                                                                                                                  >  1:628181/1‑151 (MQ=255)

            aTGCGGTAATGACTAACAAGATTTCCATTTTCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCt                                                                                                                                 <  2:169540/151‑1 (MQ=255)

               cGGTAATGACTAACAAGATTTCCATTTTCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTgcg                                                                                                                              <  2:63216/151‑1 (MQ=255)

                            cAAGATTTCCATTTTCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGt                                                                                                                  >  2:192079/1‑150 (MQ=255)

                                      aTTTTCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTc                                                                                                       >  1:299197/1‑151 (MQ=255)

                                         ttCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTAt                                                                                                    >  2:318716/1‑151 (MQ=255)

                                                cacacaGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGc                                                                                              >  2:477204/1‑150 (MQ=255)

                                                  cacaGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCAcc                                                                                           <  2:581165/151‑1 (MQ=255)

                                                       cATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTcc                                                                                       >  2:267828/1‑150 (MQ=255)

                                                        aTAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCGTCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAg                                                                                     <  2:175530/151‑1 (MQ=255)

                                                        aTAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTcc                                                                                       >  2:411420/1‑149 (MQ=255)

                                                           gagGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGa                                                                                    >  2:469495/1‑149 (MQ=255)

                                                             ggCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACtt                                                                                <  2:489395/151‑1 (MQ=255)

                                                              gCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTc                                                                               <  1:275134/151‑1 (MQ=255)

                                                                        caAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTg                                                                     <  2:353121/151‑1 (MQ=255)

                                                                           aaaaTTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGaa                                                                   >  2:607763/1‑150 (MQ=255)

                                                                              aTTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATa                                                               <  2:312711/151‑1 (MQ=255)

                                                                              aTTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATa                                                               <  2:182619/151‑1 (MQ=255)

                                                                              aTTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAAt                                                                >  1:110067/1‑150 (MQ=255)

                                                                                tttACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATaa                                                              >  1:190633/1‑150 (MQ=255)

                                                                                    cGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATaaaaaca                                                         <  1:459401/151‑1 (MQ=255)

                                                                                      cAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAAcgcg                                                                        >  1:404109/1‑134 (MQ=255)

                                                                                      cAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAAcgcg                                                                        <  2:404102/134‑1 (MQ=255)

                                                                                       aGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATaaaaacaaaa                                                      <  2:190628/151‑1 (MQ=255)

                                                                                                 ttttCATCATCAGAACCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTACCCCTGCGCGCTATTTAAGTATTTTTGATTCTATTCCGGCCCCGTCCAGACCTTCAACCGCTTTGAAAAAAAAAACAAAACCccgccg                                              <  2:556278/147‑1 (MQ=255)

                                                                                                   ttCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGc                                          >  1:508446/1‑151 (MQ=255)

                                                                                                     catcatcaGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCgg                                        >  1:180142/1‑151 (MQ=255)

                                                                                                           caGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAg                                  <  2:392036/151‑1 (MQ=255)

                                                                                                              aaTCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCCCCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTg                                <  2:578937/150‑1 (MQ=255)

                                                                                                              aaTCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGc                               >  2:133216/1‑151 (MQ=255)

                                                                                                               aTCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCg                              >  2:208424/1‑151 (MQ=255)

                                                                                                                 ccTTCCGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCggg                            >  1:590889/1‑151 (MQ=255)

                                                                                                                     ccGGATAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCg                        >  2:394708/1‑151 (MQ=255)

                                                                                                                          tAATTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTg                     >  1:589003/1‑149 (MQ=255)

                                                                                                                            aTTAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAgg                  >  2:272790/1‑150 (MQ=255)

                                                                                                                              tAGCTCTCCCCTTTAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGAt                <  1:324099/150‑1 (MQ=255)

                                                                                                                                            aaGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCCCCGTCCAGACCTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCag  <  2:483383/150‑1 (MQ=255)

CGCAAACACATAATGCGGTAATGACTAACAAGATTTCCATTTTCAACGCACACAGCATAGAGGCCATCTTCACAAAAAATTTTACGCAGTTCTTCGATGTTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAG  >  NC_000913/1644796‑1645085

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 17 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A