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 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 3,824,368 G→A pseudogene (501/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3680GA100.0% 168.7 / NA 55pseudogene (501/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (35/20);  total (35/20)

AAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACG  >  W3110S.gb/3824318‑3824432
                                                  |                                                                
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                <  1:3145416/69‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                               <  1:1529465/70‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                               <  1:3906090/70‑1 (MQ=255)
   aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCTGTATTGTAAACGGTGAAGCAATTTGCGATCt                                           >  1:4001186/1‑71 (MQ=255)
   aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                                                                >  1:2981635/1‑50 (MQ=255)
   aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                            >  1:569867/1‑70 (MQ=255)
   aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt                                           >  1:3045409/1‑71 (MQ=255)
   aCCAACCCGATGAAAGGGATGGTAGCCGAAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt                                           >  1:3262449/1‑71 (MQ=255)
       acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:838538/69‑1 (MQ=255)
       acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:3228940/69‑1 (MQ=255)
       acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:1955239/69‑1 (MQ=255)
       acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:2176847/69‑1 (MQ=255)
       acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:3584757/69‑1 (MQ=255)
        cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:154754/69‑1 (MQ=255)
           gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                   <  1:2215413/71‑1 (MQ=255)
           gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                   <  1:3075801/71‑1 (MQ=255)
           gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                   <  1:764257/71‑1 (MQ=255)
              gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                         >  1:792651/1‑46 (MQ=255)
              gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                 >  1:3656858/1‑70 (MQ=255)
              gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                 >  1:2905889/1‑70 (MQ=255)
              gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                 >  1:1067936/1‑70 (MQ=255)
              gAAAGGGATGGTAGCCGCAGTTTCTGTCGGGATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                 >  1:3806210/1‑70 (MQ=255)
               aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:2534711/70‑1 (MQ=255)
               aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:2667950/70‑1 (MQ=255)
               aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:3519229/70‑1 (MQ=255)
               aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:3860395/70‑1 (MQ=255)
                aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                <  1:1148967/69‑1 (MQ=255)
                        gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:939555/1‑71 (MQ=255)
                        gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:345405/1‑71 (MQ=255)
                        gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:560493/1‑71 (MQ=255)
                        gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:1435717/1‑71 (MQ=255)
                        gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                      >  1:3849542/1‑71 (MQ=255)
                          aGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       <  1:1172387/52‑1 (MQ=255)
                             cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCTATCTGGaa                                       >  1:3992993/1‑49 (MQ=255)
                             cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       >  1:827531/1‑49 (MQ=25)
                             cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       >  1:3339105/1‑49 (MQ=25)
                             cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                       >  1:1501502/1‑49 (MQ=25)
                             cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTAGCGATCTGGaa                                       >  1:2921406/1‑49 (MQ=255)
                                          ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa     <  1:707680/67‑1 (MQ=255)
                                          ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa     <  1:702508/67‑1 (MQ=255)
                                            taatgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc   >  1:3130143/4‑70 (MQ=255)
                                            taTTGTAAACGGTGAAGGAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:431391/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATAc                                    >  1:123897/2‑37 (MQ=16)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:705347/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:3998004/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:4127433/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:1567349/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:1974322/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:2091871/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:2453036/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:2489307/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:258543/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:270667/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:3294788/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:3286862/2‑71 (MQ=255)
                                            taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:307375/2‑71 (MQ=255)
                                            taTTGTAAACGG‑TAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg  >  1:744917/2‑70 (MQ=255)
                                                  |                                                                
AAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACG  >  W3110S.gb/3824318‑3824432

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A