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
A1 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	631,812	T→C	F640S (TTC→TCC)	cstA →	carbon starvation protein involved in peptide utilization, APC peptide transporter family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	631,812	0	T	C	100.0%	125.7 / NA	35	F640S (TTC→TCC)	cstA	carbon starvation protein involved in peptide utilization, APC peptide transporter family protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/16); total (19/16)

CGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTTCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCGAAAGAAACG  >  NC_000913/631695‑631936

cGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCgg                                                                                                         <  1:201973/139‑1 (MQ=255)

           gATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGc                                                                                                            <  1:799584/125‑1 (MQ=255)

           gATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGc                                                                                                            >  2:799584/1‑125 (MQ=255)

                                     tGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCcaacaa                                                                                                                        <  1:1013750/87‑1 (MQ=255)

                                     tGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCcaacaa                                                                                                                        >  2:1013750/1‑87 (MQ=255)

                                     tGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGc                                                                                                            <  2:905107/99‑1 (MQ=255)

                                     tGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGc                                                                                                            >  1:905107/1‑99 (MQ=255)

                                               ttCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAAcc                                                                                                  <  2:355793/99‑1 (MQ=255)

                                               ttCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAAcc                                                                                                  >  1:355793/1‑99 (MQ=255)

                                               ttCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTtct                                                          >  2:20331/1‑139 (MQ=255)

                                               ttCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTtct                                                          >  2:364362/1‑139 (MQ=255)

                                                    ggCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTAACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGAtt                                                     >  2:800235/1‑139 (MQ=255)

                                                         tGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGAc                                                <  2:743882/139‑1 (MQ=255)

                                                                           ttCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGaa                              <  1:625162/139‑1 (MQ=255)

                                                                             ccGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTtc                                                           <  1:888322/108‑1 (MQ=255)

                                                                             ccGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTtc                                                           >  2:888322/1‑108 (MQ=255)

                                                                               gTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGAt                          >  2:1062530/1‑139 (MQ=255)

                                                                                      tatgCTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTaa                                                                                                    <  2:748641/58‑1 (MQ=39)

                                                                                      tataCTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTaa                                                                                                    >  1:748641/1‑58 (MQ=255)

                                                                                      tataCTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGc                   >  1:1093085/1‑139 (MQ=255)

                                                                                        taCTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCa                 <  1:364362/139‑1 (MQ=255)

                                                                                             aGTCACAGCTGGCGCAACTGGTGTCCACCAACCGTCTGGATGCCGGGTTAACCATCTTCTATCTGGTGGACGTGGAGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCGAAAGCCAACgcc            >  2:677693/1‑137 (MQ=255)

                                                                                                cacaGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCgg                                                                                                         >  2:994997/1‑43 (MQ=255)

                                                                                                cacaGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCgg                                                                                                         <  1:994997/43‑1 (MQ=255)

                                                                                                cacaGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTCGCGGCATTGAAAGATCCGAAGCCAACGGCgaa         >  1:419387/1‑139 (MQ=255)

                                                                                                  caGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACg                                               >  2:1115768/1‑99 (MQ=255)

                                                                                                  caGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACg                                               <  1:1115768/99‑1 (MQ=255)

                                                                                                    gCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGGCGGGTTAAcc                                                                                                  >  1:360061/1‑46 (MQ=39)

                                                                                                    gCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAAcc                                                                                                  <  2:360061/46‑1 (MQ=255)

                                                                                                       ggCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAtctt                                                                                             >  2:33754/1‑48 (MQ=255)

                                                                                                       ggCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAtctt                                                                                             <  1:33754/48‑1 (MQ=255)

                                                                                                       ggCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCa                                                                 >  2:311936/1‑76 (MQ=255)

                                                                                                       ggCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCa                                                                 <  1:311936/76‑1 (MQ=255)

                                                                                                       ggCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCGAAAGAAACg  >  2:734051/1‑139 (MQ=255)

                                                                                                       ggCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCGAAAGAAACg  <  1:1062530/139‑1 (MQ=255)

CGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTTCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCGAAAGAAACG  >  NC_000913/631695‑631936

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A