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
A1 F1 I1 R1	66	20.9	912876	97.7%	891879	114.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,024,017	C→T	T17I (ACC→ATC)	rcsA →	transcriptional regulator of colanic acid capsular biosynthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,024,017	0	C	T	100.0%	85.8 / NA	26	T17I (ACC→ATC)	rcsA	transcriptional regulator of colanic acid capsular biosynthesis
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (13/13); total (13/13)

CATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAATTATCGTTACGCATTGAGTGAGGGTATGCCATGTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAACCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAGCGCCCTTCAGTGGTGTTTATTAATGAGGACTGTTTCATCCACGAT  >  NC_000913/2023881‑2024150

cATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAATTATCGTTACGCATTGAGTGAGGGTATGCCATGTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAATCg                                                                                                                                     <  2:262966/139‑1 (MQ=255)

      gTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAATTATCGTTACGCATTGAGTGAGGGTATGCCATGTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAATCGGGTATc                                                                                                                               <  1:347779/139‑1 (MQ=255)

               gttgttCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAATTATCGTTACGCATTGAGTGAGGGTATGCCATGTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAATCGGGt                                                                                                                                  >  2:89167/1‑127 (MQ=255)

               gttgttCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAATTATCGTTACGCATTGAGTGAGGGTATGCCATGTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAATCGGGt                                                                                                                                  <  1:89167/127‑1 (MQ=255)

                                tgatgaAATATTCAGGTAAGGGGAATTATCGTTACGCATTGAGTGAGGGTATGCCATGTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAaga                                                                                                     >  2:82168/1‑139 (MQ=255)

                                                                         agtgagGGTATGCCATGTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGc                                                            >  1:120536/1‑139 (MQ=255)

                                                                                   tGCCATGTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAATCGGGTATCGGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTca                                                  >  1:143584/1‑139 (MQ=255)

                                                                                         gTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTg                                                                                                                             <  1:290857/58‑1 (MQ=255)

                                                                                         gTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTg                                                                                                                             >  2:290857/1‑58 (MQ=255)

                                                                                             aCGATTATTATGGAGTTATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAGCGCCCtt                                        >  1:25266/1‑139 (MQ=255)

                                                                                                         gATTTATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAGCGCCCTTCAGTGGTGTtta                            <  2:25266/139‑1 (MQ=255)

                                                                                                         gATTTATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAGCGCCCTTCAGTGGTGTtta                            <  2:143584/139‑1 (MQ=255)

                                                                                                           tttATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGAcc                                                                      <  1:301188/95‑1 (MQ=255)

                                                                                                           tttATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGAcc                                                                      >  2:445014/1‑95 (MQ=255)

                                                                                                           tttATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGAcc                                                                      >  2:301188/1‑95 (MQ=255)

                                                                                                           tttATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGAcc                                                                      <  1:445014/95‑1 (MQ=255)

                                                                                                           tttATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAg                                               <  1:298590/118‑1 (MQ=255)

                                                                                                           tttATGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATAAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAg                                               >  2:298590/1‑118 (MQ=255)

                                                                                                              aTGTAGTTACACCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAGCGCCCTTCAGTGGTGTTTATTAAt                       >  2:341437/1‑139 (MQ=255)

                                                                                                                      acacCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGc                                                            <  1:383754/94‑1 (MQ=255)

                                                                                                                      acacCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGc                                                            >  2:383754/1‑94 (MQ=255)

                                                                                                                      acacCCGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAGCGCCCTTCAGTGGTGTTTATTAATGAGGACTg               >  1:158071/1‑139 (MQ=255)

                                                                                                                         cccGACTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAGCGCCCTTCAGTGGTGTTTATTAATGAGGACTGttt            <  1:341437/139‑1 (MQ=255)

                                                                                                                             aCTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAgc                                              >  2:111764/1‑101 (MQ=255)

                                                                                                                             aCTAGGTTTAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAgc                                              <  1:111764/101‑1 (MQ=255)

                                                                                                                                   tttAATCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAGCGCCCTTCAGTGGTGTTTATTAATGAGGACTGTTTCATCCACGAt  <  2:158071/139‑1 (MQ=255)

CATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAATTATCGTTACGCATTGAGTGAGGGTATGCCATGTCAACGATTATTATGGATTTATGTAGTTACACCCGACTAGGTTTAACCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAAGAGAAATCAACGACATTGAAACCGTTGATGACCTTGCCATAGCTTGTGATTCACAGCGCCCTTCAGTGGTGTTTATTAATGAGGACTGTTTCATCCACGAT  >  NC_000913/2023881‑2024150

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A