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
A8 F1 I1 R1	771	44.8	2153074	94.1%	2026042	109.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,316,160	G→A	891 (TAG→TAA)	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,316,160	0	G	A	100.0%	206.4 / NA	63	891 (TAG→TAA)	rcsD	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (29/34); total (29/34)

GTATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAGCAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTACAG  >  NC_000913/2316026‑2316294

gTATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAg                                                                                                                                    <  1:593080/139‑1 (MQ=255)

 tATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                                   <  1:995656/139‑1 (MQ=255)

 tATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                                   <  1:941009/139‑1 (MQ=255)

 tATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                                   >  2:389490/1‑139 (MQ=255)

 tATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                                   >  1:378084/1‑139 (MQ=255)

  aTTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGt                                                                                                                                  <  1:65600/139‑1 (MQ=255)

   tttGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTa                                                                                                                                 <  1:381308/139‑1 (MQ=255)

       ccATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCt                                                                                                                             <  1:1023812/139‑1 (MQ=255)

       ccATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCt                                                                                                                             <  1:1000629/139‑1 (MQ=255)

         aTGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTAt                                                                                                                           <  2:378084/139‑1 (MQ=255)

          tGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTAtt                                                                                                                          >  2:1040252/1‑139 (MQ=255)

                     gTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGaa                                                                                                                   <  2:604942/135‑1 (MQ=255)

                     gTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGaa                                                                                                                   >  1:604942/1‑135 (MQ=255)

                      tACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAata                                                                                                              >  2:184081/1‑139 (MQ=255)

                      tACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAata                                                                                                              >  1:904853/1‑139 (MQ=255)

                      tACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAata                                                                                                              >  2:40875/1‑139 (MQ=255)

                         ccGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACa                                                                                                                                      >  1:813187/1‑112 (MQ=255)

                          cGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGaa                                                                                                          <  2:305178/139‑1 (MQ=255)

                               aGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTaa                                                                                                     >  2:224008/1‑139 (MQ=255)

                                  aGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCt                                                                                                                             <  2:606327/112‑1 (MQ=255)

                                  aGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCt                                                                                                                             >  1:606327/1‑112 (MQ=255)

                                  aGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAatta                                                                                                  <  1:224008/139‑1 (MQ=255)

                                  aGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAatta                                                                                                  <  1:184081/139‑1 (MQ=255)

                                         tgAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGa                                                                                           >  2:285742/1‑139 (MQ=255)

                                              cGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGAcc                                                                                      <  1:285742/139‑1 (MQ=255)

                                              cGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGAcc                                                                                      <  1:934651/139‑1 (MQ=255)

                                                 tGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGc                                                                                              >  2:189882/1‑128 (MQ=255)

                                                 tGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGc                                                                                              <  1:189882/128‑1 (MQ=255)

                                                      cATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATa                                                                              <  1:1040252/139‑1 (MQ=255)

                                                                 tGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTAt                                                                                                                           >  1:1033152/1‑83 (MQ=255)

                                                                 tGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTAt                                                                                                                           <  2:1033152/83‑1 (MQ=255)

                                                                     aaGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTAtt                                                               <  2:904853/139‑1 (MQ=255)

                                                                          tGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAatta                                                                                                  >  1:387564/1‑99 (MQ=255)

                                                                          tGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAatta                                                                                                  <  2:387564/99‑1 (MQ=255)

                                                                          tGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCaa                                                          <  1:389490/139‑1 (MQ=255)

                                                                                     tAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGc                                               >  1:1065158/1‑139 (MQ=255)

                                                                                        aaaaaTACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                                   >  2:212258/1‑52 (MQ=255)

                                                                                        aaaaaTACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAgg                                                                                                                                   <  1:212258/52‑1 (MQ=255)

                                                                                               cATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTg                                     >  2:273400/1‑139 (MQ=255)

                                                                                                  cAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAata                                                                                                              >  1:1030876/1‑63 (MQ=255)

                                                                                                  cAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAata                                                                                                              <  2:1030876/63‑1 (MQ=255)

                                                                                                  cAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGt                                  >  1:911020/1‑139 (MQ=255)

                                                                                                          ttGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGAt                                                                                          <  2:799738/75‑1 (MQ=255)

                                                                                                          ttGACAGTTATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGAt                                                                                          >  1:799738/1‑75 (MQ=255)

                                                                                                                 ttATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGAt                                                                                          >  1:988722/1‑68 (MQ=255)

                                                                                                                 ttATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGAt                                                                                          <  2:988722/68‑1 (MQ=255)

                                                                                                                  tATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGt                                                                  >  2:372222/1‑91 (MQ=255)

                                                                                                                  tATGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGt                                                                  <  1:372222/91‑1 (MQ=255)

                                                                                                                   aTGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGaa                                                                                                                   <  1:563179/41‑1 (MQ=255)

                                                                                                                   aTGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGaa                                                                                                                   <  2:406709/41‑1 (MQ=255)

                                                                                                                   aTGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGaa                                                                                                                   >  1:406709/1‑41 (MQ=255)

                                                                                                                   aTGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGaa                                                                                                                   >  2:563179/1‑41 (MQ=255)

                                                                                                                    tGTCAAGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAAtt                >  2:503266/1‑139 (MQ=255)

                                                                                                                        aaGAGCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGaa            <  2:885559/139‑1 (MQ=255)

                                                                                                                         agagCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAg           >  2:166266/1‑139 (MQ=255)

                                                                                                                          gagCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGTAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGa          <  1:504787/139‑1 (MQ=255)

                                                                                                                          gagCTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGa          <  1:166266/139‑1 (MQ=255)

                                                                                                                             cTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTa                                                                 >  2:810250/1‑81 (MQ=255)

                                                                                                                             cTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTa                                                                 <  1:810250/81‑1 (MQ=255)

                                                                                                                             cTTGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGActc       >  1:830026/1‑139 (MQ=255)

                                                                                                                               tGCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTa     <  1:689558/139‑1 (MQ=255)

                                                                                                                                gCTGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATAACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTAc    >  2:530719/1‑139 (MQ=255)

                                                                                                                                  tGTAACAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTACAg  <  1:273400/139‑1 (MQ=255)

GTATTTGCCATGCTAAATCTGGTACCCGGCAAGCAGTTATGTGAAACGCTGGAACATCTGATTCGTGAGAAGGATGTTCCAGGAATAGAAAAATACATCAGCGACATTGACAGTTATGTCAAGAGCTTGCTGTAGCAAGGTAGCCTATTACATGAACAATATGAACGTAATTATTGCCGATGACCATCCGATAGTCTTGTTCGGTATTCGCAAATCACTTGAGCAAATTGAGTGGGTGAATGTTGTCGGCGAATTTGAAGACTCTACAG  >  NC_000913/2316026‑2316294

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A