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
A14 F1 I1 R1	770	68.5	3470224	91.7%	3182195	103.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	723,528	(T)_8→9	coding (887/2685 nt)	kdpD ←	fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	723,520	1	.	T	100.0%	109.7 / NA	35	R299S (CGT→AGT)	kdpD	fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (17/18); total (17/18)

TTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCG  >  NC_000913/723399‑723632

ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAg                                                                                                  <  2:494809/139‑1 (MQ=255)

   ccGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACg                                                                                                                    >  2:1696579/1‑119 (MQ=255)

   ccGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACg                                                                                                                    <  1:1696579/119‑1 (MQ=255)

   ccGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCgg                                                                                               >  1:582792/1‑139 (MQ=255)

     gagaTTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTg                                                                                             <  2:582792/139‑1 (MQ=255)

             gTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTgcagggcag                                                                                     <  1:483882/139‑1 (MQ=255)

                               cTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACcg                                                                   >  1:801802/1‑139 (MQ=255)

                                     cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAg                                                                                                  >  2:219194/1‑102 (MQ=255)

                                     cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAg                                                                                                  <  1:219194/102‑1 (MQ=255)

                                               cGCTGGATCAGAAAGTGTTGTCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTAc                                                    >  2:1019045/1‑139 (MQ=255)

                                                              tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTAc                                                    <  2:1271134/123‑1 (MQ=255)

                                                              tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTAc                                                    >  1:1271134/1‑123 (MQ=255)

                                                              tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAg                                    >  2:1299946/1‑139 (MQ=255)

                                                              tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑ttttttt                                                                                                           >  1:753513/1‑67 (MQ=255)

                                                              tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑ttttttt                                                                                                           <  2:753513/67‑1 (MQ=255)

                                                                ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgc                                   >  2:1446428/1‑139 (MQ=255)

                                                                ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTaa                                                                                                   <  1:1487054/74‑1 (MQ=255)

                                                                ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTaa                                                                                                   >  2:1487054/1‑74 (MQ=255)

                                                                ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt                                                                                >  1:1285911/1‑93 (MQ=255)

                                                                ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt                                                                                <  2:1285911/93‑1 (MQ=255)

                                                                ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGa                                                          <  1:766231/115‑1 (MQ=255)

                                                                ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGa                                                          >  2:766231/1‑115 (MQ=255)

                                                                 tGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgccg                                 <  2:801802/139‑1 (MQ=255)

                                                                   ccGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAg                                                                                                  <  2:1110416/72‑1 (MQ=255)

                                                                   ccGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAg                                                                                                  >  1:1110416/1‑72 (MQ=255)

                                                                   ccGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgccgcg                               <  1:1299946/139‑1 (MQ=255)

                                                                        tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTTCCGGTAAGCGGTgcagggca                                                                                      >  1:1547611/1‑80 (MQ=255)

                                                                        tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTTTTCCGGTAAGCGGTgcagggca                                                                                      <  2:1547611/80‑1 (MQ=255)

                                                                        tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTTCGGTAAGCGTTGCAGGGCAgggg                                                                                  <  1:1016665/83‑1 (MQ=255)

                                                                        tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAgggg                                                                                  >  2:1016665/1‑83 (MQ=255)

                                                                            cgcCCAGTTCCTGCGCCAGACCTAAGGCGCGGAGAATTGCCCGACGTTTTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTgcg                       <  1:1019045/139‑1 (MQ=255)

                                                                                       tGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGtttt           >  2:539745/1‑139 (MQ=255)

                                                                                           ccAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGc       >  2:1079001/1‑139 (MQ=255)

                                                                                            cAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCt      <  1:1079001/139‑1 (MQ=255)

                                                                                                cGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCg  <  1:382178/139‑1 (MQ=255)

                                                                                                        gcTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAg                                                                                                  >  1:986754/1‑35 (MQ=37)

                                                                                                        gcTGAGAATTGCCCGACGT‑TTTTTTTTCCGGTAAg                                                                                                  <  2:986754/35‑1 (MQ=37)

                                                                                                         cTGAGAATTGCCCGACGTTTTTTTTTTCCGGTAAGCGGTGCAGGGCAgggg                                                                                  <  2:12314/51‑1 (MQ=255)

                                                                                                         cTGAGAATTGCCCGACGTTTTTTTTTTCCGGTAAGCGGTGCAGGGCAgggg                                                                                  >  1:12314/1‑51 (MQ=255)

TTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TTTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCG  >  NC_000913/723399‑723632

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