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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	437,107	G→A	173 (TAG→TAA)	pgpA →	phosphatidylglycerophosphatase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	437,107	0	G	A	100.0%	154.5 / NA	48	173 (TAG→TAA)	pgpA	phosphatidylglycerophosphatase A
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (26/22); total (26/22)

TGGCCGATCCGCTGGTTTGATCGCAATGTGCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAGTTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTTCCGGCTTCAAAGTGATATCCACC  >  NC_000913/436973‑437242

tGGCCGATCCGCTGGTTTGATCGCAATGTGCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATtgt                                                                                                                                     >  1:370143/1‑139 (MQ=255)

                   aTCGCAATGTGCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGa                                                                                                                  >  1:225648/1‑139 (MQ=255)

                   aTCGCAATGTGCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGa                                                                                                                  <  1:923157/139‑1 (MQ=255)

                     cGCAATGTGCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACg                                                                                                                >  2:730891/1‑139 (MQ=255)

                      gCAATGTGCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTATATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGc                                                                                                               >  1:559984/1‑139 (MQ=255)

                        aaTGTGCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCtt                                                                                                             >  2:467343/1‑139 (MQ=255)

                        aaTGTGCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCtt                                                                                                             >  1:459280/1‑139 (MQ=255)

                          tgtgCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGt                                                                                                           <  2:479134/139‑1 (MQ=255)

                              cATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACg                                                                                                       >  1:559133/1‑139 (MQ=255)

                               aTGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGt                                                                                                      <  1:269516/139‑1 (MQ=255)

                                     gcATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCtcatc                                                                                                <  2:559133/139‑1 (MQ=255)

                                      cATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGAtgt                                                                                                                    <  1:192771/118‑1 (MQ=255)

                                      cATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGAtgt                                                                                                                    >  2:192771/1‑118 (MQ=255)

                                      cATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGt                                                                                                      >  2:175131/1‑132 (MQ=255)

                                      cATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGt                                                                                                      <  1:175131/132‑1 (MQ=255)

                                            gATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTg                                                                                         <  1:730891/139‑1 (MQ=255)

                                                aTGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGAct                                                                                     <  1:290518/139‑1 (MQ=255)

                                                 tGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGActc                                                                                    <  1:250399/139‑1 (MQ=255)

                                                 tGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGActc                                                                                    <  2:559984/139‑1 (MQ=255)

                                                       acgaTATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTAttt                                                                              >  1:465621/1‑139 (MQ=255)

                                                       acgaTATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTAttt                                                                              >  1:869371/1‑139 (MQ=255)

                                                        cgaTATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTa                                                                             <  2:370143/139‑1 (MQ=255)

                                                        cgaTATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTa                                                                             <  2:274520/139‑1 (MQ=255)

                                                                  gCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGt                                                                                                           >  2:360165/1‑99 (MQ=255)

                                                                  gCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGt                                                                                                           <  1:360165/99‑1 (MQ=255)

                                                                     ggggTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAg                                                                >  1:313695/1‑139 (MQ=255)

                                                                                  cAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGt                                                                                                      <  1:840119/88‑1 (MQ=255)

                                                                                  cAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGt                                                                                                      >  2:840119/1‑88 (MQ=255)

                                                                                     gCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACgg                                                >  2:90041/1‑139 (MQ=255)

                                                                                     gCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACgg                                                >  1:516831/1‑139 (MQ=255)

                                                                                        tCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCtcat                                                                                                 <  1:691925/87‑1 (MQ=255)

                                                                                        tCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCtcat                                                                                                 >  2:691925/1‑87 (MQ=255)

                                                                                                 ttATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGt                                                                                                      <  2:395604/73‑1 (MQ=255)

                                                                                                 ttATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGt                                                                                                      >  1:395604/1‑73 (MQ=255)

                                                                                                   aTCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCgg                                  >  2:233503/1‑139 (MQ=255)

                                                                                                   aTCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCgg                                  >  1:355608/1‑139 (MQ=255)

                                                                                                                   cGCTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTTCCGGCtt                  <  1:233503/139‑1 (MQ=255)

                                                                                                                     cTGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTTCCGGCTTCa                <  1:750663/139‑1 (MQ=255)

                                                                                                                      tGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTa                                                                             >  1:464908/1‑77 (MQ=255)

                                                                                                                      tGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTa                                                                             <  2:464908/77‑1 (MQ=255)

                                                                                                                      tGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTTCCGGCTTCaa               >  2:244026/1‑139 (MQ=255)

                                                                                                                      tGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTTCCGGCTTCa                <  1:929208/138‑1 (MQ=255)

                                                                                                                      tGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTTCCGGCTTCa                >  2:929208/1‑138 (MQ=255)

                                                                                                                      tGGGTATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTCCCGGCTTCaa               >  2:459629/1‑139 (MQ=255)

                                                                                                                          tATTCTGTCGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTTCCGGCTTCAAAGTg           <  2:465621/139‑1 (MQ=255)

                                                                                                                                  cGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCtcat                                                                                                 <  2:853996/45‑1 (MQ=255)

                                                                                                                                  cGTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCtcat                                                                                                 >  1:853996/1‑45 (MQ=255)

                                                                                                                                   gTAATTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTTCCGGCTTCAAAGTGATATCCAcc  >  2:168758/1‑139 (MQ=255)

TGGCCGATCCGCTGGTTTGATCGCAATGTGCATGGCGGCATGGGGATCATGATCGACGATATTGTCGCCGGGGTGATTTCCGCAGGCATCCTGTATTTTATCGGTCATCACTGGCCGCTGGGTATTCTGTCGTAGTTGTGCACCGATGCCTGATGTGACGCTTGTCACGTCTCATCAGGCCTGGACTCTTATTTAAATCCTACGACAGGATGCGGTTTATACGGCGTTTCCAGTTCGGCAATCTGTTCCGGCTTCAAAGTGATATCCACC  >  NC_000913/436973‑437242

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A