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
A23 F107 I1 R1	19	39.5	1386814	92.9%	1288350	143.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	3,317,435	A→C	L31R (CTG→CGG)	nusA ←	transcription termination/antitermination L factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	3,317,435	0	A	C	94.9%	108.1 / NA	39	L31R (CTG→CGG)	nusA	transcription termination/antitermination L factor
Reads supporting (aligned to +/- strand): ref base A (0/0); major base C (14/23); minor base T (0/2); total (14/25)
Fisher's exact test for biased strand distribution p-value = 5.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGCTTCAAGGGTGATTTCCTTGGTCGGCTGGGTGACTTCATCAACAACTAACCAGCGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCAGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGACTATTAAAAGTGGGGAACCAGGTTCG  >  NC_000913_3_pae_tpiA/3317289‑3317576

cGGCTTCAAGGGTGATTTCCTTGGTCGGCTGGGTGACTTCATCAACAACTAACCAGCGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCgc                                                                                                                                             <  1:619795/149‑1 (MQ=255)

   cTTCAAGGGTGATTTCCTTGGTCGGCTGGGTGACTTCATCAACAACTAACCAGCGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCcgcgcg                                                                                                                                          >  2:242525/1‑149 (MQ=255)

   cTTCAAGGGTGATTTCCTTGGTCGGCTGGGTGACTTCATCAACAACTAACCAGCGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTATTTGTTGCTGTCGCCcgcgcg                                                                                                                                          >  2:635468/1‑149 (MQ=255)

    ttCAAGGGTGATTTCCTTGGTCGGCTGGGTGACTTCATCAACAACTAACCAGCGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCgcgcgc                                                                                                                                         >  2:335923/1‑149 (MQ=255)

           gTGATTTCCTTGGTCGGCTGGGTGACTGCGTCAACAACTAACCGGCGACGGAAAGTGTCAAAATCACCGGTTTTGCGGTCGGTCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTCGCTGGCGTGTGGGCGCTTTCCaa                                                                                                                                  <  2:431039/149‑1 (MQ=255)

                           gCTGGGTGACTTCATCAACAACTAACCGGCGACGGAAAGTGTCTAAATCACCGCTTTTGCGATCGATCTGTACCCGGACGTCGACCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAAtcttc                                                                                                                  <  2:17918/149‑1 (MQ=255)

                             tGGGTGACTTCATCAACAACTAACCAGCGACGGAAAGTGTCAAAATCACCGTTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTtctc                                                                                                                <  1:238400/149‑1 (MQ=255)

                                 tGACTTCATCAACAACTAACCAGGGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGa                                                                                                            <  2:393495/149‑1 (MQ=255)

                                           aacaacTAACCAGCGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTTTTTTTTTCTGTCGCCCACGCGCTTTCCAATGCTTCGAAAATCTTCTTGCCCGGTAGCGCCt                                                                                                  >  2:160542/1‑149 (MQ=255)

                                                 tAACCACCGACGGAAAGTGTCAAAATCACCACTTATGCGATCGAACTGTACGCGGACGTCGATCTCTTGTTCATATTTTTCCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCAt                                                                                            <  1:291332/149‑1 (MQ=255)

                                                  aaCCAGCGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCAtt                                                                                           <  1:582873/149‑1 (MQ=255)

                                                    ccAGCGACGGAAAGTGTCAAAATCACCACTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTgg                                                                                         >  1:378050/1‑149 (MQ=255)

                                                      aGCGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGAGCTTTCCAATGCTTCGAAAATCTTCTCGGGAGTTAGGGCCTTTTCCTTGGAt                                                                                       >  1:601732/1‑149 (MQ=255)

                                                        cGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGCTTTCCAGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATAc                                                                                     <  1:335923/149‑1 (MQ=255)

                                                              aaaGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTc                                                                               <  1:466276/149‑1 (MQ=255)

                                                              aaaGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTCCTCGCGAGGAAGCGCCTTTTCATTGGATACGGCTTc                                                                               >  1:632140/1‑149 (MQ=255)

                                                                    tCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTAc                                                                         <  1:242525/149‑1 (MQ=255)

                                                                     cAAAATCCCCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACa                                                                        <  1:325874/149‑1 (MQ=255)

                                                                      aaaaTCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGGCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGGGGTAGCGCCTTTTCATTGGAGACGGCTTCAACTagag                                                                       >  1:240352/1‑149 (MQ=255)

                                                                         aTCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGa                                                                                                            >  2:662419/1‑109 (MQ=255)

                                                                         aTCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGa                                                                                                            <  1:662419/109‑1 (MQ=255)

                                                                            aCCGGTTTTGTGATCGATCTGTACGCGGAGGTCGATCTCTTGTTCATATTTTTTCTTTGTTGTTGTCGTCCGCGCGGTTTCCATTGCTTCGTAAATCTTCTGGCGGGGTAGCGCCTTTTCGTTGTGTACGGCTTCAACTACCGTCaaga                                                                 >  2:375966/1‑147 (MQ=255)

                                                                               gCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTCGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAAttt                                                              <  2:525299/149‑1 (MQ=255)

                                                                                   ttGCGATCTATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCttt                                                          <  1:148908/149‑1 (MQ=255)

                                                                                   gtGCGATCGTGCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCttt                                                          <  1:686713/148‑1 (MQ=255)

                                                                                                          gTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTc                                   >  1:386832/1‑149 (MQ=255)

                                                                                                                ctctTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAg                             <  1:39730/149‑1 (MQ=255)

                                                                                                                 tcctGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGa                            <  1:71854/146‑1 (MQ=255)

                                                                                                                  ctTGTTCATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGAc                           <  2:405373/149‑1 (MQ=255)

                                                                                                                    tGTTCATATTTTCTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGACTa                         <  2:427372/149‑1 (MQ=255)

                                                                                                                      ttCATATTTTTTTTTTTTTTTTGTCGCCCGCGCGCTTTCCAATGCTTCGGAAATCTTCGCGCGTGGTAGCGCCTTTTCATTGGATACGGCTTCAACTATATCCATATTTTCTTTGTTCTTCGCTGGCTTTTCACCTCATGCAGTCTAtt                       >  2:531778/1‑149 (MQ=255)

                                                                                                                      ttCATATTTTTTCTTTGCTGCTGTCGCCCGCGCGCTTTCCATTGCTTCGAAAAACTTCTCGCGAGGTAGCGCCTTTTCATTGGTTACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGACTAtt                       <  2:295433/149‑1 (MQ=255)

                                                                                                                        cATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATg                                                                                                                                <  1:570372/42‑1 (MQ=255)

                                                                                                                        cATATTTTTTCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATg                                                                                                                                >  2:570372/1‑42 (MQ=255)

                                                                                                                              ttttCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGACTCTTGAAAGTgg               >  1:363206/1‑149 (MQ=255)

                                                                                                                              ttttCTTTGTTGCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGACTCGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGACTATTAAAAGTgg               <  1:444025/149‑1 (MQ=255)

                                                                                                                               tttCGTTGTTGCTGCCGCCTGCGCGCTTTCCAATGCTTCGAAAATCTGCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGACAAGATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGACTATTAAAAGTggg              <  1:411251/149‑1 (MQ=255)

                                                                                                                                    ttgttgCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGACTATTAAAAGTGGGGAAcc         <  2:188322/149‑1 (MQ=255)

                                                                                                                                    ttgttgCTGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTAAAGCCAAAATTTCTTTGTTCATAGCGGGCTTTTAACGTCATCCAGACTATTAAGAGCGCGGAAcc         >  2:650800/1‑149 (MQ=255)

                                                                                                                                        tgCTGTCGCCCGCGCGCCTTCCAACGCCTCGAAAATCTTCTCGCGAGGTAGTGTCTTTTCATTTGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATTGCGGGCTTTTCTCCTCATCCAGAATATTAAAAGTGGGGAACCAGGt     <  2:187670/149‑1 (MQ=255)

                                                                                                                                           tGTCGCCCGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGACTATTAAAAGTGGGGAACCAGGTTCg  >  1:401384/1‑149 (MQ=255)

CGGCTTCAAGGGTGATTTCCTTGGTCGGCTGGGTGACTTCATCAACAACTAACCAGCGACGGAAAGTGTCAAAATCACCGCTTTTGCGATCGATCTGTACGCGGACGTCGATCTCTTGTTCATATTTTTTCTTTGTTGCTGTCGCCAGCGCGCTTTCCAATGCTTCGAAAATCTTCTCGCGAGGTAGCGCCTTTTCATTGGATACGGCTTCAACTACAGCCAAAATTTCTTTGTTCATCGCGGGCTTTTCACCTCATCCAGACTATTAAAAGTGGGGAACCAGGTTCG  >  NC_000913_3_pae_tpiA/3317289‑3317576

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