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
A0 F0 I1 R1 61 39.0 4165548 97.4% 4057243 49.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_017635 2,312,962 T→C G139G (GGA→GGG)  ECW_RS11560 ← phage tail sheath protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0176352,312,9620TC100.0% 24.7 / NA 18G139G (GGA→GGG) ECW_RS11560phage tail sheath protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/7);  total (11/7)

ACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGTCCCGGCACGCCGAGAATACGCGGTTTAACACCGGTTACCGACT  >  NC_017635/2312924‑2313005
                                      |                                           
aCTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCAcac                                   >  1:1217846/1‑47 (MQ=11)
 cTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACAcc                                  >  2:687820/1‑49 (MQ=11)
  tGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACAcc                                  >  1:489362/1‑48 (MQ=11)
       ccAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAt                            <  1:1755133/49‑1 (MQ=11)
               aCAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGtt                    >  1:424003/1‑49 (MQ=11)
                 aGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTaa                 >  1:1610065/1‑50 (MQ=11)
                 aGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTaa                 >  2:313821/1‑50 (MQ=11)
                    cACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAacac              >  2:1655002/1‑50 (MQ=11)
                     aCCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACAcc             <  2:980621/50‑1 (MQ=11)
                     aCCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACAcc             <  2:1937795/50‑1 (MQ=11)
                     aCCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACAcc             <  1:747575/50‑1 (MQ=11)
                     aCCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACAcc             <  1:564634/50‑1 (MQ=11)
                         ctTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGt          >  1:2053110/1‑49 (MQ=11)
                            tGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTAcc      >  1:1149883/1‑50 (MQ=11)
                             ggTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTAcc      <  2:1153857/49‑1 (MQ=11)
                              gTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTACCg     <  1:679295/49‑1 (MQ=11)
                               tATCCAGCCCCTGCACACCAAGAATACGCGGTTTAACACCGGTTACCGAc   >  2:1206768/1‑50 (MQ=11)
                                aTCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTACCGAct  >  1:323762/1‑50 (MQ=11)
                                      |                                           
ACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGTCCCGGCACGCCGAGAATACGCGGTTTAACACCGGTTACCGACT  >  NC_017635/2312924‑2313005

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGTCCCGGCACGCCGAGAATACGCGGTTTAACACCGGTTACCGACTC  >  NC_017635/2312924‑2313006
                                      |                                            
ACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACC                                   >  M01420:85:000000000‑AC936:1:2103:11318:15682/1‑50 (MQ=13)
  TGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACacca                                  >  M01420:85:000000000‑AC936:1:1107:13001:17269/1‑45 (MQ=25)
      GCCAGTGCAACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAAT                             <  M01420:85:000000000‑AC936:1:2110:28371:20562/50‑1 (MQ=11)
               ACAGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTT                    >  M01420:85:000000000‑AC936:1:1106:14036:19814/1‑50 (MQ=44)
                 AGCCACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAAC                 >  M01420:85:000000000‑AC936:1:2108:20257:22189/1‑51 (MQ=47)
                    CACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACC              <  M01420:85:000000000‑AC936:1:1108:6847:17854/51‑1 (MQ=11)
                    CACCTCTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACC              <  M01420:85:000000000‑AC936:1:1111:8806:6257/51‑1 (MQ=11)
                         CTTTGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTT          >  M01420:85:000000000‑AC936:1:2114:19897:17976/1‑50 (MQ=11)
                            TGGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTACCG      >  M01420:85:000000000‑AC936:1:2102:4222:17456/1‑51 (MQ=11)
                             GGTATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTACCG      <  M01420:85:000000000‑AC936:1:1110:16246:8121/50‑1 (MQ=8)
                                ATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTACCGACTC  >  M01420:85:000000000‑AC936:1:1105:14666:12192/1‑51 (MQ=0)
                                ATCCAGCCCCGGCACACCAAGAATACGCGGTTTAACACCGGTTACCGACT   <  M01420:85:000000000‑AC936:1:2107:16391:26925/50‑1 (MQ=0)
                                      |                                            
ACTGATGCCAGTGCAACAGCCACCTCTTTGGTATCCAGTCCCGGCACGCCGAGAATACGCGGTTTAACACCGGTTACCGACTC  >  NC_017635/2312924‑2313006

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑