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	3,405,012	A→G	pseudogene (281/300 nt)	yrdE →	pseudogene, yedZ paralog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,405,012	0	A	G	97.8%	169.6 / ‑4.2	46	pseudogene (281/300 nt)	yrdE	pseudogene, yedZ paralog
Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (21/24); total (22/24)
Fisher's exact test for biased strand distribution p-value = 4.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

AATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTATAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAATCGTT  >  NC_000913/3404873‑3405159

aaTCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTcc                                                                                                                                          <  1:183876/151‑1 (MQ=255)

aaTCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTc                                                                                                                                           <  2:377566/150‑1 (MQ=255)

   ccccAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGt                                                                                                                                        <  1:396610/150‑1 (MQ=255)

     ccAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCg                                                                                                                                      >  1:580137/1‑150 (MQ=255)

        gCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCgatga                                                                                                                                  <  1:404129/151‑1 (MQ=255)

          aaCCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGatgatg                                                                                                                                >  1:328600/1‑151 (MQ=255)

             cGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGgcg                                                                                                                             <  2:111808/151‑1 (MQ=255)

             cGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGgcg                                                                                                                             >  2:548099/1‑151 (MQ=255)

                          cgtcTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGa                                                                                                                 <  2:285679/150‑1 (MQ=255)

                           gtcTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAAt                                                                                                               <  1:607420/151‑1 (MQ=255)

                               aTCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAAtt                                                                                                              <  2:380205/148‑1 (MQ=255)

                                         gATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCttgttg                                                                                                 >  2:237335/1‑151 (MQ=255)

                                            ccTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCa                                                                                               <  1:507055/150‑1 (MQ=255)

                                            ccTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCa                                                                                               <  2:247965/150‑1 (MQ=255)

                                               ggCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCaaa                                                                                             <  1:90011/149‑1 (MQ=255)

                                                      cTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGgt                                                                                    >  1:94100/1‑151 (MQ=255)

                                                        aCATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGgtgt                                                                                  >  1:250895/1‑151 (MQ=255)

                                                         cATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGtt                                                                                 >  1:61770/1‑151 (MQ=255)

                                                             attTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGaa                                                                              <  1:324373/150‑1 (MQ=255)

                                                              tttGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAgg                                                                            >  2:135406/1‑151 (MQ=255)

                                                                   ggTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTAtt                                                                       <  1:397415/151‑1 (MQ=255)

                                                                   ggTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTAt                                                                        <  2:404684/150‑1 (MQ=255)

                                                                          gAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGt                                                                >  2:387876/1‑151 (MQ=255)

                                                                             gATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAg                                                             <  1:534571/151‑1 (MQ=255)

                                                                              aTTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGc                                                            <  2:148414/151‑1 (MQ=255)

                                                                               ttATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCt                                                           >  2:522660/1‑151 (MQ=255)

                                                                                tATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTg                                                          >  1:612678/1‑151 (MQ=255)

                                                                                 aTCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGt                                                         >  1:478633/1‑151 (MQ=255)

                                                                                    tcATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTg                                                       >  2:396795/1‑150 (MQ=255)

                                                                                        tGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTAt                                                  >  1:511718/1‑151 (MQ=255)

                                                                                          cAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCt                                                <  2:252894/151‑1 (MQ=255)

                                                                                              cccTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCCAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTccc                                            >  2:480422/1‑151 (MQ=255)

                                                                                               ccTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCt                                           <  2:419668/151‑1 (MQ=255)

                                                                                                cTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTg                                          >  1:229113/1‑151 (MQ=255)

                                                                                                  cATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTg                                          <  2:488240/149‑1 (MQ=255)

                                                                                                  cATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGa                                         <  2:528633/150‑1 (MQ=255)

                                                                                                  cATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGAt                                        >  2:338941/1‑151 (MQ=255)

                                                                                                                tggctTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTAttt                           >  2:179487/1‑150 (MQ=255)

                                                                                                                 ggctTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTa                          <  1:393659/150‑1 (MQ=255)

                                                                                                                        cagcttttcaCCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGACa                   <  1:387736/150‑1 (MQ=255)

                                                                                                                           cttttcaCCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTg               >  1:51421/1‑151 (MQ=255)

                                                                                                                              ttcaCCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCt             <  2:194079/150‑1 (MQ=255)

                                                                                                                                   cTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGaa        >  1:564842/1‑150 (MQ=255)

                                                                                                                                    ttACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAAt      >  2:351029/1‑151 (MQ=255)

                                                                                                                                     tACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAAt      <  1:418144/150‑1 (MQ=255)

                                                                                                                                         ttATAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAATCGtt  >  2:288838/1‑150 (MQ=255)

AATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTATAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAATCGTT  >  NC_000913/3404873‑3405159

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A