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 I2 R1	765	53.2	2691310	93.4%	2513683	103.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,002,224	(G)_7→8	coding (418/1071 nt)	elfG →	putative fimbrial‑like adhesin protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,002,217	1	.	G	93.5%	100.6 / 0.4	31	coding (411/1071 nt)	elfG	putative fimbrial‑like adhesin protein
Reads supporting (aligned to +/- strand): ref base . (1/1); new base G (16/13); total (17/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.71e-01

TGGGCATTCGCCGCGGATTCACCGTTAGTCTATTTAGGCGACAACTGGTACAAAATTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACA‑GGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTCCCTGAAAATATTGCAGCCGTTCGTTGGCTCGGTCGTC  >  NC_000913/1002080‑1002340

tGGGCATTCGCCGCGGATTCACCGTTAGTCTATTTAGGCGACAACTGGTACAAAATTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACA‑g                                                                                                                            >  2:1306768/1‑139 (MQ=255)

                                     gCGACAACTGGTACAAAATTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGa                                                                                                              <  1:1003709/117‑1 (MQ=255)

                                     gCGACAACTGGTACAAAATTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGa                                                                                                              >  2:1003709/1‑117 (MQ=255)

                                       gACAACTGGTACAAAATTAATGACTATCTTGCCGCAAAAACTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGCCACAGGGGGGGGATACCCGATGGCATATTTGCGACCATGGCGGt                                                                                      >  2:1113717/1‑139 (MQ=255)

                                          aaCTGGTACAAAATTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCaa                                                                                   >  1:495566/1‑139 (MQ=255)

                                               gTACAAAATTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCa                                                                                                         <  1:590309/112‑1 (MQ=255)

                                               gTACAAAATTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCa                                                                                                         >  2:590309/1‑112 (MQ=255)

                                                 aCAAAATTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAg                                                                            <  2:615262/139‑1 (MQ=255)

                                                   aaaaTTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGt                                                                          >  1:499752/1‑139 (MQ=255)

                                                          aTGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACA‑GGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAggg                                                                  >  2:1057604/1‑139 (MQ=255)

                                                                  cTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACA‑GGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCg                                                          <  1:1057604/139‑1 (MQ=255)

                                                                         ccAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGa                                                                                                              <  1:715454/81‑1 (MQ=255)

                                                                         ccAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGa                                                                                                              >  2:715454/1‑81 (MQ=255)

                                                                           aaaGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAAt                                                     >  2:683682/1‑136 (MQ=255)

                                                                           aaaGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAAt                                                     <  1:683682/136‑1 (MQ=255)

                                                                                         ggTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGt                                                                          >  2:653579/1‑101 (MQ=255)

                                                                                         ggTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGt                                                                          <  1:653579/101‑1 (MQ=255)

                                                                                                     ttCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATAcc                                                                                                                 >  2:960408/1‑50 (MQ=255)

                                                                                                     ttCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATAcc                                                                                                                 <  1:960408/50‑1 (MQ=255)

                                                                                                               gCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGa                                                                                                              >  2:193440/1‑43 (MQ=255)

                                                                                                               gCGGTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGa                                                                                                              <  1:193440/43‑1 (MQ=255)

                                                                                                                  gTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTccc                                     >  1:930338/1‑113 (MQ=255)

                                                                                                                  gTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTccc                                     <  2:930338/113‑1 (MQ=255)

                                                                                                                  gTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTCCCTGAAAATATTGCAGCCGTTTGTTGGc           >  1:581663/1‑139 (MQ=255)

                                                                                                                  gTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTCCCTGAAAATATTGCAGCCGTTCGTTGGc           >  2:130612/1‑139 (MQ=255)

                                                                                                                  gTTCCTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTCCCTGAAAATATTGCAGCCGTTCGTTGGc           >  2:280524/1‑139 (MQ=255)

                                                                                                                     ccTTTCGAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTCCCTGAAAATATTGCAGCCGTTCGTTGGCTCg        <  2:499752/139‑1 (MQ=255)

                                                                                                                           gAAAACGTGGGCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTCCCTGAAAATATTGCAGCCGTTCGTTGGCTCGgtcgtc  <  2:1091947/139‑1 (MQ=255)

                                                                                                                                   gggCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCttt                                         <  1:683816/92‑1 (MQ=255)

                                                                                                                                   gggCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCttt                                         >  2:683816/1‑92 (MQ=255)

                                                                                                                                    ggCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAg                                                                            >  1:697042/1‑56 (MQ=255)

                                                                                                                                    ggCACAGGGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAg                                                                            <  2:697042/56‑1 (MQ=255)

TGGGCATTCGCCGCGGATTCACCGTTAGTCTATTTAGGCGACAACTGGTACAAAATTAATGACTATCTTGCCGCCAAAGTTTTATTGCAGGTTAAAGGCAGTTCTCCTACTGCGGTTCCTTTCGAAAACGTGGGCACA‑GGGGGGGATACCCGATGGCATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTCCCTGAAAATATTGCAGCCGTTCGTTGGCTCGGTCGTC  >  NC_000913/1002080‑1002340

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