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
A21 F73 I1 R1	19	39.3	1399748	93.9%	1314363	140.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	3,440,923	C→T	G36D (GGC→GAC)	rpoA ←	RNA polymerase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	3,440,923	0	C	T	95.2%	118.2 / ‑6.0	42	G36D (GGC→GAC)	rpoA	RNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (20/20); total (21/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGG  >  NC_000913_3_pae_tpiA/3440778‑3441062

gTTGAGCAGGATGTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTCCTCATGTAGTACACCATCAATCTCAACCTCGGTCCCCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGGATGGTCaa                                                                                                                                          >  1:539112/1‑149 (MQ=255)

     gCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCa                                                                                                                                     >  2:505295/1‑149 (MQ=255)

      cAGGATTTCCAGGATATCTTCCTGAACGCCTTCTCTGGTGCTGTACTCATGTAGTGCACCATCTATCTCAACCTCGGTCACCGCTCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCAc                                                                                                                                    <  1:621963/149‑1 (MQ=255)

       aGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACg                                                                                                                                   <  2:223502/149‑1 (MQ=255)

               cAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAg                                                                                                                           <  1:228063/149‑1 (MQ=255)

                 ggATATCTTCCTGAACGCCTTCTTTGGGGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGc                                                                                                                         <  2:133626/149‑1 (MQ=255)

                      tCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCCGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAg                                                                                                                    >  1:331057/1‑149 (MQ=255)

                      tCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAg                                                                                                                    >  1:434861/1‑149 (MQ=255)

                       cTTCCTGAACGCCTTCTTGGGTGCTCTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCACCGACGAGCGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAgg                                                                                                                   <  1:561365/149‑1 (MQ=255)

                        ttCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCCATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAggg                                                                                                                  >  1:318947/1‑149 (MQ=255)

                         tCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGCGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGt                                                                                                                 <  2:227581/149‑1 (MQ=255)

                             gAACGCCTTCTTTGGTGCTGTACTCATGTAGTCCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGACTGGCTGAGAGCAGAATACGGCGCAGTGCGTTACACACAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCAcc                                                                                                             <  2:289677/149‑1 (MQ=255)

                                   cttcttTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCCCGCTCTAAAGGCTCAAGGGTCACCTTGgcg                                                                                                       >  1:92914/1‑149 (MQ=255)

                                      cttTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGgcgtgc                                                                                                    <  2:504690/149‑1 (MQ=255)

                                            ttcTGTCCTCATGTAGTACACCAGCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGGATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGaa                                                                                              <  1:407184/147‑1 (MQ=255)

                                              cTGTACTCATGTAGTAAACCATCAATCTCAACCTCGGGCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACACAGAGTATAGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACt                                                                                            <  2:466869/149‑1 (MQ=255)

                                                 tACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCAc                                                                                         >  2:680952/1‑149 (MQ=255)

                                                    tCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTg                                                                                      >  2:570924/1‑149 (MQ=255)

                                                        gtagtaCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCg                                                                                  >  1:239615/1‑149 (MQ=255)

                                                           gtaCACCATCAACCTCAGCCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCCCTTGCTCGata                                                                               <  2:518932/149‑1 (MQ=255)

                                                            taCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGCCGTGCGTCGAACTCACTTGCTCGattc                                                                              >  2:298586/1‑147 (MQ=255)

                                                             acacCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGAAGAATACGGCGCAGTGCGTTACTCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCCAGGGTCACATTGGCGTGCGTAGACCTGACTTGCTCGATATc                                                                             >  1:258982/1‑149 (MQ=255)

                                                              cacCCTCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAACCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCa                                                                            <  1:557717/149‑1 (MQ=255)

                                                              cacCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCa                                                                            >  1:445781/1‑149 (MQ=255)

                                                                ccATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAATTCACTTGCTCGTTTTCAAc                                                                          >  2:591913/1‑149 (MQ=255)

                                                                           aaCCTCGGTCACCGCGCAACCCGGCATCGATGAGACCTCGATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGtt                                                               >  1:519398/1‑149 (MQ=255)

                                                                              cTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTa                                                            <  1:465252/149‑1 (MQ=255)

                                                                               tCGGTCCCCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTGTAg                                                           >  1:198736/1‑149 (MQ=255)

                                                                                  gTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGaaa                                                        >  2:646763/1‑149 (MQ=255)

                                                                                   tCACCGCGCAACCCGGCATGGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAAc                                                       <  2:82465/149‑1 (MQ=255)

                                                                                     aCCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAActc                                                     >  1:174338/1‑149 (MQ=255)

                                                                                       cgcgCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTg                                                   >  1:155695/1‑149 (MQ=255)

                                                                                        gcgcAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCGTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGt                                                  <  1:391632/149‑1 (MQ=255)

                                                                                        gcgcAACCCGGCATCGATGAGAGCAGAATACGCCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGt                                                  <  1:82658/149‑1 (MQ=255)

                                                                                                    aTCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTg                                      >  1:524061/1‑149 (MQ=255)

                                                                                                      cGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCa                                    <  1:224897/149‑1 (MQ=255)

                                                                                                       gATGAGATCAGAATACGGCGTAGTGCGTTAACCAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCAt                                   <  1:335098/149‑1 (MQ=255)

                                                                                                                       ggCGCAGTGGGTTACCCAGAGTATGGTCAAAGCCACGCTCTAAAAGCTCAAGGGTCACCTTTGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTgg                   <  2:621506/149‑1 (MQ=255)

                                                                                                                                cGTGACCCAGAGTATGGTCAAAGCCACGCGCTAAAGGGTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCt          <  2:198736/149‑1 (MQ=255)

                                                                                                                                      ccAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCATGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACtt    >  2:306407/1‑149 (MQ=255)

                                                                                                                                       cAGAGTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTg   <  2:651747/149‑1 (MQ=255)

                                                                                                                                        agagTATGGTCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTgg  >  1:182205/1‑149 (MQ=255)

GTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGG  >  NC_000913_3_pae_tpiA/3440778‑3441062

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A