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
A9 F1 I2 R1	78	48.0	2243616	94.8%	2126947	114.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,313,434	T→C	intergenic (+258/‑54)	micF → / → rcsD	sRNA antisense regulator affecting ompF expression, Hfq‑dependent/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	2,313,434	0	T	C	100.0%	199.9 / NA	54	intergenic (+258/‑54)	micF/rcsD	sRNA antisense regulator affecting ompF expression, Hfq‑dependent/phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (31/23); total (31/23)

GCTTTTTGTAGGTTATTTGTACAGCAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGTACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATC  >  NC_000913/2313309‑2313568

gCTTTTTGTAGGTTATTTGTACAGCAAAATGGTGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTg                                                                                                                           >  2:779103/1‑139 (MQ=255)

gCTTTTTGTAGGTTATTTGTACAGCAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTg                                                                                                                           >  1:1004526/1‑139 (MQ=255)

gCTTTTTGTAGGTTATTTGTACAGCAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTg                                                                                                                           <  1:952787/139‑1 (MQ=255)

              aTTTGTACAGCAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGTAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTcgc                                                                                                             >  2:250888/1‑139 (MQ=255)

              aTTTGTACAGCAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTcgc                                                                                                             <  1:639091/139‑1 (MQ=255)

               tttGTACAGCAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTcgcg                                                                                                            <  1:781623/139‑1 (MQ=255)

                      aGCAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGtttt                                                                                                     >  1:861880/1‑139 (MQ=255)

                        cAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTcgc                                                                                                             <  2:44553/129‑1 (MQ=255)

                        cAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTcgc                                                                                                             >  1:44553/1‑129 (MQ=255)

                        cAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTaa                                                                                                   >  2:311030/1‑139 (MQ=255)

                        cAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTaa                                                                                                   <  2:1004526/139‑1 (MQ=255)

                        cAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTaa                                                                                                   >  1:981419/1‑139 (MQ=255)

                        cAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTaa                                                                                                   >  1:340638/1‑139 (MQ=255)

                         aaaaTGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAAc                                                                                                  <  1:1054484/139‑1 (MQ=255)

                         aaaaTGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAAc                                                                                                  <  2:340638/139‑1 (MQ=255)

                                  cTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTcgcg                                                                                                            >  2:254528/1‑120 (MQ=255)

                                  cTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTcgcg                                                                                                            <  1:254528/120‑1 (MQ=255)

                                     gTACATCTATTTCCCCCAATGCAGGATGATAAGTATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAaca                                                                                      >  1:551231/1‑139 (MQ=255)

                                         aTCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGaa                                                                                  <  2:981419/139‑1 (MQ=255)

                                              tttCCCCCAATGCAGGATGATAAATATCACGGGAGAGTAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGt                                                                             <  2:702251/139‑1 (MQ=255)

                                                tCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCa                                                                           >  2:1081554/1‑139 (MQ=255)

                                                   cccAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAAGCCGTCAGaa                                                                        >  1:1089555/1‑139 (MQ=255)

                                                     cAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAag                                                                      >  1:284476/1‑139 (MQ=255)

                                                      aaTGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAaga                                                                     >  1:340137/1‑139 (MQ=255)

                                                        tGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAgaga                                                                   >  1:629968/1‑139 (MQ=255)

                                                        tGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAgaga                                                                   >  2:655330/1‑139 (MQ=255)

                                                           aGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTaa                                                                                                   <  1:329119/104‑1 (MQ=255)

                                                           aGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTaa                                                                                                   >  2:329119/1‑104 (MQ=255)

                                                            ggATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAAc                                                               >  1:168737/1‑139 (MQ=255)

                                                             gatgatAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGt                                                                             >  2:1065210/1‑124 (MQ=255)

                                                             gatgatAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGt                                                                             >  2:910201/1‑124 (MQ=255)

                                                             gatgatAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGt                                                                             <  1:1065210/124‑1 (MQ=255)

                                                             gatgatAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGt                                                                             <  1:910201/124‑1 (MQ=255)

                                                                  tAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCAc                                                         >  2:974713/1‑139 (MQ=255)

                                                                  tAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCAc                                                         >  2:920508/1‑139 (MQ=255)

                                                                       atCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGAccc                                                    <  1:974713/139‑1 (MQ=255)

                                                                           cGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCtt                                                >  2:762726/1‑139 (MQ=255)

                                                                                        aaTCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCAc                                           <  2:950675/131‑1 (MQ=255)

                                                                                        aaTCATCAATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCAc                                           >  1:950675/1‑131 (MQ=255)

                                                                                          tcatcaATCAGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCggg                                 <  2:861880/139‑1 (MQ=255)

                                                                                             tcaatcaGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAAt                                                                                 >  2:1091372/1‑88 (MQ=255)

                                                                                             tcaatcaGGTAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAAt                                                                                 <  1:1091372/88‑1 (MQ=255)

                                                                                                      tAAGAGTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCg                     >  1:502162/1‑139 (MQ=255)

                                                                                                        agagTCTGGAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGct                   <  2:502162/139‑1 (MQ=255)

                                                                                                               ggAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACg                                                        >  1:1102652/1‑95 (MQ=255)

                                                                                                               ggAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACg                                                        <  2:1102652/95‑1 (MQ=255)

                                                                                                               ggAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCttttt            >  1:85654/1‑139 (MQ=255)

                                                                                                               ggAATTTCACACTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCtattt            >  2:842242/1‑139 (MQ=255)

                                                                                                                     tCACACTTCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGGCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGtt      <  2:1120462/139‑1 (MQ=255)

                                                                                                                      cacaCTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTg     >  2:209023/1‑139 (MQ=255)

                                                                                                                      cacaCTGCACCCTTTATACTGCCCTATCACTTCGAGAAGTTTTAACAGGGCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTg     >  1:685937/1‑139 (MQ=255)

                                                                                                                        cacTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGAt   <  1:842242/139‑1 (MQ=255)

                                                                                                                        cacTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGAt   <  2:154270/139‑1 (MQ=255)

                                                                                                                         acTGCACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATc  <  1:920508/139‑1 (MQ=255)

GCTTTTTGTAGGTTATTTGTACAGCAAAATGGCGCTTGTACATCTATTTCCCCCAATGCAGGATGATAAATATCACGGGAGAATAGAGAATCATCAATCAGGTAAGAGTCTGGAATTTCACACTGTACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATC  >  NC_000913/2313309‑2313568

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