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
A5 F84 I0 R1	42	46.2	1977590	90.0%	1779831	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	753,346	T→G	63.8%	I375L (ATT→CTT)	gltA ←	citrate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	753,346	0	T	G	63.8%	14.8 / 24.3	32	I375L (ATT→CTT)	gltA	citrate synthase
Reads supporting (aligned to +/- strand): ref base T (8/3); new base G (5/15); total (13/19)
Fisher's exact test for biased strand distribution p-value = 2.09e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.09e-01

TTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTC  >  NC_000913/753216‑753488

ttttCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCttt                                                                                                                                    >  1:582931/1‑143 (MQ=255)

     atatCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGga                                                                                                                               >  1:170041/1‑143 (MQ=255)

     atatCCTGGATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGga                                                                                                                               <  1:216031/143‑1 (MQ=255)

               taCGGCTGACGCAGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAGGACGGAAGACCCATCGCTTTCAGGATGATACCaga                                                                                                                     <  2:683873/143‑1 (MQ=255)

                  aGCTGACGCGGCCGGGCAAACTTCAGACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTa                                                                                                                  <  2:385582/143‑1 (MQ=255)

                    cggACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCGCTTGGTACTTTCCACAGCAACCATCACTTTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGa                                                                                                                <  1:228439/141‑1 (MQ=255)

                      gACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGaaa                                                                                                              <  1:694573/143‑1 (MQ=255)

                        cgcgGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATc                                                                                                            <  1:775470/143‑1 (MQ=255)

                             aCGCGCGATCTTCATGCCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGt                                                                                                       <  2:396421/143‑1 (MQ=255)

                               gggCCATCGTCATACCGTCACTGTGCAGTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAATTTTACTGTTAACATTGAAGACGGAAGACCTATCGCTTTTAGGATGATACCAGAGTAGAAATCGACGTTc                                                                                                     <  1:214707/143‑1 (MQ=255)

                                 gCAATCTTCATGCCGGCACTGTGCATTGCGCCCCGGTGGGCGATCCAGCCAACGGTACGGGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTGCAGGATGATACCAGAGTAGAAATCGACGTTCgg                                                                                                   <  1:58290/143‑1 (MQ=255)

                                   taTCTTCATTCCGCGTCAGGGCATTTCGTTCCAGTGAGGGATCCAGCGAATGGTACGTGCCATTGCGAGAATGACGGTGAACATGGAAGGAGGAAGACCAATTGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGt                                                                                                 <  2:96409/142‑1 (MQ=255)

                                       ttCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAg                                                                                             >  1:665924/1‑143 (MQ=255)

                                        tCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGCGAACATGGAAGACGGAATACCCGTCGCTTCCAGGATGATACCAGAGTAGAAATCGACGATCGAGTACAGt                                                                                            >  2:205750/1‑143 (MQ=255)

                                                          gttCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTAc                                                                          <  1:62474/142‑1 (MQ=255)

                                                                   aGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTc                                                                 <  1:962896/143‑1 (MQ=255)

                                                                          gATCAAGCCAACGGGACGTGCCATTGCTAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGa                                                          <  2:80534/143‑1 (MQ=255)

                                                                                   aaCGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTcga                                                 >  1:923868/1‑141 (MQ=255)

                                                                                           gTGCCGTTGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATa                                         <  2:129436/143‑1 (MQ=255)

                                                                                            tGCCATTGCGTAAATGACGGTGAACATTGAAGACGGACGACCCTTCGGTTTCAGGATGATACCAGGGTAGAGATCGACGCTCGGGCACAGTTTATTCTCGAAAAAGTACGGGACGTTCAGCGCGATGTTTTCCAGCCCCATAg                                        >  2:341244/1‑143 (MQ=255)

                                                                                            tGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGCTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCAtcg                                        >  1:322157/1‑141 (MQ=255)

                                                                                                 ttGCGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACt                                   >  1:753479/1‑143 (MQ=255)

                                                                                                   gggAAAATGACGCTGAACATGGAAGACGGAATACCCATCGCGTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTc                                 <  2:236809/141‑1 (MQ=255)

                                                                                                    cGAAAATGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGAGGTTTTCCAGCCCCACAGCCACTTcg                                >  1:312813/1‑142 (MQ=255)

                                                                                                          tGACGGTGAACATGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAgg                          <  1:912872/143‑1 (MQ=255)

                                                                                                          tGACGGTGAACATGGAACACGACACACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGATGTTCGGGGACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAgg                          <  1:249866/143‑1 (MQ=255)

                                                                                                               gTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTCAAGCCGGTCATc                     >  2:761099/1‑143 (MQ=255)

                                                                                                               gTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTGTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTACATAGCCACTTCcagcacgcgatc                     >  2:663683/1‑136 (MQ=255)

                                                                                                               gTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGATCGGGTACAGTTTCTTCTCGATAAAGTACGTGTAGTTCAGTGCGATGTTTTCTTGCTTTATTGCTTATTCCTGCAGGTTATc                     >  1:429614/1‑143 (MQ=255)

                                                                                                               gTGAACATGGAAGACGGAAGACCCCTCGCTTTCGGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCAGAGCCACTTCCAGCAGGTCATc                     <  2:942488/143‑1 (MQ=255)

                                                                                                                 gAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGCTGTTTTCCAGATCCATAGCCACTTCCAGCAGGTCATCCt                   >  1:564020/1‑143 (MQ=255)

                                                                                                                   acctGGAAGACGGAAGACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTc                 <  1:385951/140‑1 (MQ=255)

                                                                                                                                  tACCCATCGCGTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTc  <  2:361099/143‑1 (MQ=255)

TTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTC  >  NC_000913/753216‑753488

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A