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
A11 F1 I2 R1	760	67.6	3323148	92.7%	3080558	109.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,134,823	G→A	231 (TAG→TAA)	yghT →	putative ATP‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,134,823	0	G	A	100.0%	116.4 / NA	37	231 (TAG→TAA)	yghT	putative ATP‑binding protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (16/21); total (16/21)

CCATAACGCCACAGTTAACCTTTGGTGGTGCACAACTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCGTGGTTATCACTAGTCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTGCCGCCGGTAAAGTAAATACCCACGCCAT  >  NC_000913/3134693‑3134949

ccATAACGCCACAGTTAACCTTTGGTGGTGCACAACTGGTGGATTACGATGCCAACCAGACACTGGAACAGGTGCTGGTTGATGCAGAAAAAGCGATTACGGAATACATGACAGCGCG‑GGGAAGCACTAATCAAAAATg                                                                                                                         >  2:33125/1‑139 (MQ=255)

          acaGTTAACCTTTGGTGGTGCACAACTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCg                                                                                                               <  2:597508/139‑1 (MQ=255)

          acaGTTAACCTTTGGTGGTGCACAACTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCg                                                                                                               <  1:33125/139‑1 (MQ=255)

              ttAACCTTTGGTGGTGCACAACTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCg                                                                                                           >  1:1442617/1‑139 (MQ=255)

              ttAACCTTTGGTGGTGCACAACTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCg                                                                                                           >  2:1257124/1‑139 (MQ=255)

                aaCCTTTGGTGGTGCACAACTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGa                                                                                                                       >  1:1547317/1‑125 (MQ=255)

                aaCCTTTGGTGGTGCACAACTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGa                                                                                                                       <  2:1547317/125‑1 (MQ=255)

                                   cTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAgg                                                                                      <  1:1149838/139‑1 (MQ=255)

                                   cTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGAGTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAgg                                                                                      <  2:1188579/139‑1 (MQ=255)

                                      gTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCg                                                                                                               >  2:926138/1‑111 (MQ=255)

                                      gTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCg                                                                                                               <  1:926138/111‑1 (MQ=255)

                                        tGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGt                                                                                 <  2:731561/139‑1 (MQ=255)

                                              cGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑Tc                                                                         <  2:1556771/139‑1 (MQ=255)

                                                aTGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCaa                                                                       >  2:509964/1‑139 (MQ=255)

                                                        cAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATg                                                               <  1:894299/139‑1 (MQ=255)

                                                        cAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATg                                                               <  2:1624580/139‑1 (MQ=255)

                                                           ccACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAAGGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTa                                                            >  2:1015147/1‑139 (MQ=255)

                                                             aCTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATc                                                          <  2:1442617/139‑1 (MQ=255)

                                                               tGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCa                                                        >  2:44650/1‑139 (MQ=255)

                                                                       gtgtTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGcc                                                >  2:1071642/1‑139 (MQ=255)

                                                                          ttggttgATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCccac                                             <  1:509964/139‑1 (MQ=255)

                                                                           tggttgATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGaaa                                                                                                                     >  1:411702/1‑68 (MQ=255)

                                                                           tggttgATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGaaa                                                                                                                     <  2:411702/68‑1 (MQ=255)

                                                                            ggttgATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCccacca                                           >  1:1375396/1‑139 (MQ=255)

                                                                                                  aCGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTGCCGCCGgta                     <  2:762756/139‑1 (MQ=255)

                                                                                                   cGGATTTTATGACCGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTGCCGCCGgtaa                    <  1:519620/139‑1 (MQ=255)

                                                                                                               ccGCGCG‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTGCCGCCGGTAAAGTAAATACCCa        <  2:1375396/139‑1 (MQ=255)

                                                                                                                cgcgcg‑GGTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGTAGATTAAA‑‑TCAACTGCAATGCTATGCAGTACAGCCCACCAGAAAGAAAAATTGCCGCCGGTAAAGTAAATACCCAc       <  1:1015147/139‑1 (MQ=255)

                                                                                                                   cgcgggTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAATCTCAACTGCAATg                                                               >  2:1633887/5‑83 (MQ=255)

                                                                                                                   cgcgggTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAATCTCAACTGCAATg                                                               <  1:1633887/79‑1 (MQ=255)

                                                                                                                   cgcgggTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTgcc                            >  1:977472/5‑116 (MQ=255)

                                                                                                                   cgcgggTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTgcc                            <  2:977472/112‑1 (MQ=255)

                                                                                                                   cgcgggTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTGCCGCCGGTAAAGTAAATACCCACGc     >  2:1588768/5‑139 (MQ=255)

                                                                                                                   cgcgggTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGATAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTGCCGCCGGTAAAGTAAATACCCACGc     >  2:1598098/5‑139 (MQ=255)

                                                                                                                     cgggTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAgg                                                                                      >  2:1011839/3‑58 (MQ=255)

                                                                                                                     cgggTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCAGTTTCAgg                                                                                      <  1:1011839/56‑1 (MQ=255)

                                                                                                                      gggTTATCACTAATCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTGCCGCCGGTAAAGTAAATACCCACGCCAt  <  1:1588768/138‑1 (MQ=255)

CCATAACGCCACAGTTAACCTTTGGTGGTGCACAACTGGTTGATATCGATGCCAATCAGCCACTGGAACAGGTGTTGGTTGATGCAGAAAAAGCGATTACGGATTTTATGACCGCGCGTGGTTATCACTAGTCAAAAATGGAAATGCCCGATCGCCAGGACCGGGCATTTTCAGGAAGGTTAAA‑‑TCAACTGCAATGCTATCCAGTACAGCCCACCAGAAAGAAAAATTGCCGCCGGTAAAGTAAATACCCACGCCAT  >  NC_000913/3134693‑3134949

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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